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Chilimoniuk J, Erol A, Rödiger S, Burdukiewicz M. Challenges and opportunities in processing NanoString nCounter data. Comput Struct Biotechnol J 2024; 23:1951-1958. [PMID: 38736697 PMCID: PMC11087919 DOI: 10.1016/j.csbj.2024.04.061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 04/25/2024] [Accepted: 04/25/2024] [Indexed: 05/14/2024] Open
Abstract
NanoString nCounter is a medium-throughput technology used in mRNA and miRNA differential expression studies. It offers several advantages, including the absence of an amplification step and the ability to analyze low-grade samples. Despite its considerable strengths, the popularity of the nCounter platform in experimental research stabilized in 2022 and 2023, and this trend may continue in the upcoming years. Such stagnation could potentially be attributed to the absence of a standardized analytical pipeline or the indication of optimal processing methods for nCounter data analysis. To standardize the description of the nCounter data analysis workflow, we divided it into five distinct steps: data pre-processing, quality control, background correction, normalization and differential expression analysis. Next, we evaluated eleven R packages dedicated to nCounter data processing to point out functionalities belonging to these steps and provide comments on their applications in studies of mRNA and miRNA samples.
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Affiliation(s)
| | - Anna Erol
- Clinical Research Centre, Medical University of Białystok, Białystok, Poland
| | - Stefan Rödiger
- Institute of Biotechnology, Faculty Environment and Natural Sciences, Brandenburg University of Technology Cottbus - Senftenberg, Senftenberg, Germany
| | - Michał Burdukiewicz
- Clinical Research Centre, Medical University of Białystok, Białystok, Poland
- Institute of Biotechnology and Biomedicine, Autonomous University of Barcelona, Barcelona, Spain
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2
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Gastier-Foster JM, Lutwama F, Mbabazi O, Mlenga S, Ulaya K, Namazzi R, Hollingsworth EF, Lopez-Terrada D, Fisher KE, Roy A, Allen CE, Poplack DG, Mzikamanda R, Ozuah N, Wasswa P. Rapid gene fusion testing using the NanoString nCounter platform to improve pediatric leukemia diagnoses in Sub-Saharan Africa. Front Oncol 2024; 14:1426638. [PMID: 38939333 PMCID: PMC11208450 DOI: 10.3389/fonc.2024.1426638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Accepted: 05/31/2024] [Indexed: 06/29/2024] Open
Abstract
Risk stratification and molecular targeting have been key to increasing cure rates for pediatric cancers in high-income countries. In contrast, precise diagnosis in low-resource settings is hindered by insufficient pathology infrastructure. The Global HOPE program aims to improve outcomes for pediatric cancer in Sub-Saharan Africa (SSA) by building local clinical care and diagnostic capacity. This study aimed to assess the feasibility of implementing molecular assays to improve leukemia diagnoses in SSA. Custom NanoString nCounter gene fusion assays, previously validated in the US, were used to test samples from suspected leukemia patients. The NanoString platform was chosen due to relatively low cost, minimal technical and bioinformatics expertise required, ability to test sub-optimal RNA, and rapid turnaround time. Fusion results were analyzed blindly, then compared to morphology and flow cytometry results. Of 117 leukemia samples, 74 were fusion-positive, 30 were negative, 7 were not interpretable, and 6 failed RNA quality. Nine additional samples were negative for leukemia by flow cytometry and negative for gene fusions. All 74 gene fusions aligned with the immunophenotype determined by flow cytometry. Fourteen samples had additional information available to further confirm the accuracy of the gene fusion results. The testing provided a more precise diagnosis in >60% of cases, and 9 cases were identified that could be treated with an available tyrosine kinase inhibitor, if detected at diagnosis. As risk-stratified and targeted therapies become more available in SSA, implementing this testing in real-time will enable the treatment of pediatric cancer to move toward incorporating risk stratification for optimized therapy.
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Affiliation(s)
- Julie M. Gastier-Foster
- Global HOPE, Texas Children’s Hospital, Houston, TX, United States
- Department of Pathology, Texas Children’s Hospital, Houston, TX, United States
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, United States
| | - Fredrick Lutwama
- Biomedical Research Centre, Makerere University, Kampala, Uganda
| | - Olive Mbabazi
- Biomedical Research Centre, Makerere University, Kampala, Uganda
| | - Steven Mlenga
- Baylor College of Medicine Children’s Foundation - Malawi, Lilongwe, Malawi
| | - Kennedy Ulaya
- Baylor College of Medicine Children’s Foundation - Malawi, Lilongwe, Malawi
| | - Ruth Namazzi
- College of Health Sciences, Makerere University, Kampala, Uganda
| | - E. Faith Hollingsworth
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, United States
| | - Dolores Lopez-Terrada
- Department of Pathology, Texas Children’s Hospital, Houston, TX, United States
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, United States
| | - Kevin E. Fisher
- Department of Pathology, Texas Children’s Hospital, Houston, TX, United States
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, United States
| | - Angshumoy Roy
- Department of Pathology, Texas Children’s Hospital, Houston, TX, United States
- Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX, United States
| | - Carl E. Allen
- Global HOPE, Texas Children’s Hospital, Houston, TX, United States
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
| | - David G. Poplack
- Global HOPE, Texas Children’s Hospital, Houston, TX, United States
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
| | - Rizine Mzikamanda
- Baylor College of Medicine Children’s Foundation - Malawi, Lilongwe, Malawi
| | - Nmazuo Ozuah
- Global HOPE, Texas Children’s Hospital, Houston, TX, United States
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
| | - Peter Wasswa
- Global HOPE, Texas Children’s Hospital, Houston, TX, United States
- Department of Pediatrics, Baylor College of Medicine, Houston, TX, United States
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3
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Marchiò C, Criscitiello C, Scatena C, Santinelli A, Graziano P, Malapelle U, Cursano G, Venetis K, Fanelli GN, Pepe F, Berrino E, De Angelis C, Perrone G, Curigliano G, Fusco N. Think "HER2" different: integrative diagnostic approaches for HER2-low breast cancer. Pathologica 2023; 115:292-301. [PMID: 38180137 PMCID: PMC10767801 DOI: 10.32074/1591-951x-942] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 01/06/2024] Open
Abstract
This work explores the complex field of HER2 testing in the HER2-low breast cancer era, with a focus on methodological aspects. We aim to propose clear positions to scientific societies, institutions, pathologists, and oncologists to guide and shape the appropriate diagnostic strategies for HER2-low breast cancer. The fundamental question at hand is whether the necessary tools to effectively translate our knowledge about HER2 into practical diagnostic schemes for the lower spectrum of expression are available. Our investigation is centered on the significance of distinguishing between an immunohistochemistry (IHC) score 0 and score 1+ in light of the clinical implications now apparent, as patients with HER2-low breast cancer become eligible for trastuzumab-deruxtecan treatment. Furthermore, we discuss the definition of HER2-low beyond its conventional boundaries and assess the reliability of established diagnostic procedures designed at a time when therapeutic perspectives were non-existent for these cases. In this regard, we examine potential complementary technologies, such as gene expression analysis and liquid biopsy. Ultimately, we consider the potential role of artificial intelligence (AI) in the field of digital pathology and its integration into HER2 testing, with a particular emphasis on its application in the context of HER2-low breast cancer.
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Affiliation(s)
- Caterina Marchiò
- Division of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Carmen Criscitiello
- Division of Early Drug Development for Innovative Therapy, IEO, European Institute of Oncology, IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Cristian Scatena
- Department of Laboratory Medicine, Pisa University Hospital, Anatomic Pathology 1 Universitaria, Pisa, Italy
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Italy
| | - Alfredo Santinelli
- Anatomic Pathology, Azienda Sanitaria Territoriale di Pesaro-Urbino, Pesaro, Italy
| | - Paolo Graziano
- Pathology Unit, Fondazione IRCCS Ospedale ‘Casa Sollievo della Sofferenza’, San Giovanni Rotondo (FG), Italy
| | - Umberto Malapelle
- Department of Public Health, Federico II University of Naples, Naples, Italy
| | - Giulia Cursano
- Division of Pathology, IEO, European Institute of Oncology, IRCCS, Milan, Italy
| | | | - Giuseppe Nicolò Fanelli
- Department of Laboratory Medicine, Pisa University Hospital, Anatomic Pathology 1 Universitaria, Pisa, Italy
- Department of Translational Research and New Technologies in Medicine and Surgery, University of Pisa, Italy
| | - Francesco Pepe
- Department of Public Health, Federico II University of Naples, Naples, Italy
| | - Enrico Berrino
- Division of Pathology, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Carmine De Angelis
- Department of Clinical Medicine and Surgery, Federico II University of Naples, Naples, Italy
| | - Giuseppe Perrone
- Department of Medicine and Surgery, Research Unit of Anatomical Pathology, Università Campus Bio-Medico di Roma, Roma, Italy
- Anatomical Pathology Operative Research Unit, Fondazione Policlinico Universitario Campus Bio-Medico, Roma, Italy
| | - Giuseppe Curigliano
- Division of Early Drug Development for Innovative Therapy, IEO, European Institute of Oncology, IRCCS, Milan, Italy
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
| | - Nicola Fusco
- Department of Oncology and Hemato-Oncology, University of Milan, Milan, Italy
- Division of Pathology, IEO, European Institute of Oncology, IRCCS, Milan, Italy
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Vázquez-Mosquera ME, González-Vioque E, Barbosa-Gouveia S, Bellido-Guerrero D, Tejera-Pérez C, Martinez-Olmos MA, Fernández-Pombo A, Castaño-González LA, Chans-Gerpe R, Couce ML. Transcriptomic analysis of patients with clinical suspicion of maturity-onset diabetes of the young (MODY) with a negative genetic diagnosis. Orphanet J Rare Dis 2022; 17:105. [PMID: 35246208 PMCID: PMC8896342 DOI: 10.1186/s13023-022-02263-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 02/20/2022] [Indexed: 12/04/2022] Open
Abstract
Background Diagnosis of mature-onset diabetes of the young (MODY), a non-autoimmune monogenic form of diabetes mellitus, is confirmed by genetic testing. However, a positive genetic diagnosis is achieved in only around 50% of patients with clinical characteristics of this disease. Results We evaluated the diagnostic utility of transcriptomic analysis in patients with clinical suspicion of MODY but a negative genetic diagnosis. Using Nanostring nCounter technology, we conducted transcriptomic analysis of 19 MODY-associated genes in peripheral blood samples from 19 patients and 8 healthy controls. Normalized gene expression was compared between patients and controls and correlated with each patient’s biochemical and clinical variables. Z-scores were calculated to identify significant changes in gene expression in patients versus controls. Only 7 of the genes analyzed were detected in peripheral blood. HADH expression was significantly lower in patients versus controls. Among patients with suspected MODY, GLIS3 expression was higher in obese versus normal-weight patients, and in patients aged < 25 versus > 25 years at diabetes onset. Significant alteration with respect to controls of any gene was observed in 57.9% of patients. Conclusions Although blood does not seem to be a suitable sample for transcriptomic analysis of patients with suspected MODY, in our study, we detected expression alterations in some of the genes studied in almost 58% of patients. That opens the door for future studies that can clarify the molecular cause of the clinic of these patients and thus be able to maintain a more specific follow-up and treatment in each case. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-022-02263-3.
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Affiliation(s)
- María E Vázquez-Mosquera
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain.,Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain.,Universidad de Santiago de Compostela, Santiago de Compostela, Spain.,European Reference Network for Hereditary Metabolic Disorders (MetabERN), Padova, Italy
| | - Emiliano González-Vioque
- Division of Clinical Biochemistry, Hospital Universitario Puerta de Hierro-Majadahonda, Madrid, Spain
| | - Sofía Barbosa-Gouveia
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain.,Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain.,Universidad de Santiago de Compostela, Santiago de Compostela, Spain.,European Reference Network for Hereditary Metabolic Disorders (MetabERN), Padova, Italy
| | | | - Cristina Tejera-Pérez
- Division of Endocrinology, Complejo Hospitalario Universitario de Ferrol, Ferrol, Spain
| | - Miguel A Martinez-Olmos
- Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain.,Universidad de Santiago de Compostela, Santiago de Compostela, Spain.,Division of Endocrinology and Nutrition, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBERobn), Madrid, Spain
| | - Antía Fernández-Pombo
- Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain.,Universidad de Santiago de Compostela, Santiago de Compostela, Spain.,Division of Endocrinology and Nutrition, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Fisiopatología de la Obesidad y Nutrición (CIBERobn), Madrid, Spain
| | - Luis A Castaño-González
- Endocrinology and Diabetes Research Group, Instituto de Investigación Sanitaria BioCruces, Barakaldo, Spain
| | - Roi Chans-Gerpe
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain.,Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain.,Universidad de Santiago de Compostela, Santiago de Compostela, Spain.,European Reference Network for Hereditary Metabolic Disorders (MetabERN), Padova, Italy
| | - María L Couce
- Unit of Diagnosis and Treatment of Congenital Metabolic Diseases, Hospital Clínico Universitario de Santiago de Compostela, Santiago de Compostela, Spain. .,Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain. .,Universidad de Santiago de Compostela, Santiago de Compostela, Spain. .,European Reference Network for Hereditary Metabolic Disorders (MetabERN), Padova, Italy.
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Mesonephric-like Adenocarcinoma of the Uterine Corpus: Comprehensive Immunohistochemical Analyses Using Markers for Mesonephric, Endometrioid and Serous Tumors. Diagnostics (Basel) 2021; 11:diagnostics11112042. [PMID: 34829389 PMCID: PMC8625485 DOI: 10.3390/diagnostics11112042] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 01/06/2023] Open
Abstract
Mesonephric-like adenocarcinoma (MLA) of the uterine corpus is a rare but distinct malignant tumor of the female genital tract, demonstrating a characteristic morphology and unique immunohistochemical profiles and molecular alterations. We conducted immunohistochemical staining (IHC) to make precise differential diagnoses of uterine MLAs from common histological subtypes of endometrial carcinomas. We collected 25 uterine MLAs and performed IHC for GATA3, TTF1, CD10, ER, PR, p16, p53, and HER2. Seventeen cases (68.0%) showed at least moderate nuclear GATA3 immunoreactivity in ≥25% of tumor cells. Most cases expressed TTF1 (17/21, 81.0%) and CD10 (luminal; 17/21, 81.0%). Heterogeneous TTF1 expression was noted in 12 cases. An inverse pattern of GATA3 and TTF1 staining was observed in eight cases (32.0%). Three cases (12.0%) showed moderate-to-strong ER expression in ≥25% of tumor cells, and two cases (8.0%) showed moderate-to-strong PR expression in ≥5% of tumor cells. These hormone receptor-positive MLAs varied in intensity and proportion of GATA3 staining. None of the 25 cases exhibited either diffuse and strong p16 expression or aberrant p53 expression. Five cases (20.0%) showed equivocal HER2 immunoreactivity (score 2+), but HER2 FISH confirmed that none of them exhibited HER2 gene amplification. In summary, a small subset of uterine MLAs displayed atypical IHC results: focal but strong expression of ER or PR, the complete absence of GATA3 immunoreactivity, the concurrent expression of mesonephric and hormone receptors, and the inverse pattern of GATA3 and TTF1 staining. These unusual immunophenotypes may complicate the differential diagnosis of MLA. Moreover, pathologists should be encouraged to interpret the IHC results cautiously.
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6
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Ma C, Hunt JB, Kovalenko A, Liang H, Selenica MLB, Orr MB, Zhang B, Gensel JC, Feola DJ, Gordon MN, Morgan D, Bickford PC, Lee DC. Myeloid Arginase 1 Insufficiency Exacerbates Amyloid-β Associated Neurodegenerative Pathways and Glial Signatures in a Mouse Model of Alzheimer's Disease: A Targeted Transcriptome Analysis. Front Immunol 2021; 12:628156. [PMID: 34046031 PMCID: PMC8144303 DOI: 10.3389/fimmu.2021.628156] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 04/12/2021] [Indexed: 12/22/2022] Open
Abstract
Brain myeloid cells, include infiltrating macrophages and resident microglia, play an essential role in responding to and inducing neurodegenerative diseases, such as Alzheimer's disease (AD). Genome-wide association studies (GWAS) implicate many AD casual and risk genes enriched in brain myeloid cells. Coordinated arginine metabolism through arginase 1 (Arg1) is critical for brain myeloid cells to perform biological functions, whereas dysregulated arginine metabolism disrupts them. Altered arginine metabolism is proposed as a new biomarker pathway for AD. We previously reported Arg1 deficiency in myeloid biased cells using lysozyme M (LysM) promoter-driven deletion worsened amyloidosis-related neuropathology and behavioral impairment. However, it remains unclear how Arg1 deficiency in these cells impacts the whole brain to promote amyloidosis. Herein, we aim to determine how Arg1 deficiency driven by LysM restriction during amyloidosis affects fundamental neurodegenerative pathways at the transcriptome level. By applying several bioinformatic tools and analyses, we found that amyloid-β (Aβ) stimulated transcriptomic signatures in autophagy-related pathways and myeloid cells' inflammatory response. At the same time, myeloid Arg1 deficiency during amyloidosis promoted gene signatures of lipid metabolism, myelination, and migration of myeloid cells. Focusing on Aβ associated glial transcriptomic signatures, we found myeloid Arg1 deficiency up-regulated glial gene transcripts that positively correlated with Aβ plaque burden. We also observed that Aβ preferentially activated disease-associated microglial signatures to increase phagocytic response, whereas myeloid Arg1 deficiency selectively promoted homeostatic microglial signature that is non-phagocytic. These transcriptomic findings suggest a critical role for proper Arg1 function during normal and pathological challenges associated with amyloidosis. Furthermore, understanding pathways that govern Arg1 metabolism may provide new therapeutic opportunities to rebalance immune function and improve microglia/macrophage fitness.
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Affiliation(s)
- Chao Ma
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
- Sanders-Brown Center on Aging, Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY, United States
| | - Jerry B. Hunt
- Sanders-Brown Center on Aging, Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, United States
| | - Andrii Kovalenko
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, United States
| | - Huimin Liang
- Sanders-Brown Center on Aging, Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, United States
| | - Maj-Linda B. Selenica
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, United States
- Sanders-Brown Center on Aging, Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, KY, United States
| | - Michael B. Orr
- Spinal Cord and Brain Injury Research Center, Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, United States
| | - Bei Zhang
- Spinal Cord and Brain Injury Research Center, Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, United States
- Center for Neurogenetics, Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, Cornell University, New York, NY, United States
| | - John C. Gensel
- Spinal Cord and Brain Injury Research Center, Department of Physiology, College of Medicine, University of Kentucky, Lexington, KY, United States
| | - David J. Feola
- Department of Pharmacy Practice and Science, College of Pharmacy, University of Kentucky, Lexington, KY, United States
| | - Marcia N. Gordon
- Department of Translational Neuroscience, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Dave Morgan
- Department of Translational Neuroscience, College of Human Medicine, Michigan State University, Grand Rapids, MI, United States
| | - Paula C. Bickford
- Department of Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
- Center of Excellence for Aging and Brain Repair, Department of Neurosurgery and Brain Repair, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
- Research Service, James A. Haley Veterans Affairs Hospital, Tampa, FL, United States
| | - Daniel C. Lee
- Sanders-Brown Center on Aging, Department of Neuroscience, College of Medicine, University of Kentucky, Lexington, KY, United States
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL, United States
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Yeong J, Suteja L, Simoni Y, Lau KW, Tan AC, Li HH, Lim S, Loh JH, Wee FYT, Nerurkar SN, Takano A, Tan EH, Lim TKH, Newell EW, Tan DSW. Intratumoral CD39 +CD8 + T Cells Predict Response to Programmed Cell Death Protein-1 or Programmed Death Ligand-1 Blockade in Patients With NSCLC. J Thorac Oncol 2021; 16:1349-1358. [PMID: 33975004 DOI: 10.1016/j.jtho.2021.04.016] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 04/09/2021] [Accepted: 04/30/2021] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Programmed cell death protein-1 (PD-1) and programmed death-ligand 1 (PD-L1) blockade is currently widely used in the treatment of metastatic NSCLC. Despite available biomarker stratification, clinical responses vary. Thus, the search for novel biomarkers with improved response prediction is ongoing. Previously, using mass cytometry or cytometry by time-of-flight (CyTOF), our group demonstrated that CD39+CD8+ immune cells represent tumor antigen-specific, cytotoxic T cells in treatment-naive NSCLC. We hypothesized that accurate quantitation of this T cell subset would predict immunotherapy outcome. METHODS To translate this to a clinical setting, the present study compared CyTOF data with a range of clinically relevant methods, including conventional immunohistochemistry (IHC), multiplex IHC or immunofluorescence (mIHC), and gene expression assay by NanoString. RESULTS Quantification using mIHC but not conventional IHC or NanoString correlated with the CyTOF results. The specificity and sensitivity of mIHC were then evaluated in a separate retrospective NSCLC cohort. CD39+CD8+ T cell proportion, as determined by mIHC, successfully stratified responders and nonresponders to PD-1 or PD-L1 inhibitors (objective response rate of 63.6%, compared with 0% for the negative group). This predictive capability was independent from other confounding factors, such as total CD8+ T cell proportion, CD39+ lymphocyte proportion, PD-L1 positivity, EGFR mutation status, and other clinicopathologic parameters. CONCLUSIONS Our results suggest that the mIHC platform is a clinically relevant method to evaluate CD39+CD8+ T cell proportion and that this marker can serve as a potential biomarker that predicts response to PD-1 or PD-L1 blockade in patients with NSCLC. Further validation in additional NSCLC cohorts is warranted.
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Affiliation(s)
- Joe Yeong
- Institute of Molecular Cell Biology (IMCB), Agency for Science, Technology and Research (A∗STAR), Singapore; Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore; Division of Pathology, Singapore General Hospital, Singapore
| | - Lisda Suteja
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Yannick Simoni
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Kah Weng Lau
- Institute of Molecular Cell Biology (IMCB), Agency for Science, Technology and Research (A∗STAR), Singapore; Division of Pathology, Singapore General Hospital, Singapore
| | - Aaron C Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Hui Hua Li
- Division of Medicine, Singapore General Hospital, Singapore; Centre for Quantitative Medicine, Duke-NUS Medical School, Singapore
| | - Sherlly Lim
- Institute of Molecular Cell Biology (IMCB), Agency for Science, Technology and Research (A∗STAR), Singapore
| | - Jie Hua Loh
- Division of Pathology, Singapore General Hospital, Singapore
| | - Felicia Y T Wee
- Division of Pathology, Singapore General Hospital, Singapore
| | | | - Angela Takano
- Division of Pathology, Singapore General Hospital, Singapore
| | - Eng Huat Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore
| | - Tony K H Lim
- Division of Pathology, Singapore General Hospital, Singapore
| | - Evan W Newell
- Singapore Immunology Network (SIgN), Agency for Science, Technology and Research (A∗STAR), Singapore; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Daniel S W Tan
- Division of Medical Oncology, National Cancer Centre Singapore, Singapore.
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8
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Toulza F, Dominy K, Cook T, Galliford J, Beadle J, McLean A, Roufosse C. Technical considerations when designing a gene expression panel for renal transplant diagnosis. Sci Rep 2020; 10:17909. [PMID: 33087822 PMCID: PMC7578804 DOI: 10.1038/s41598-020-74794-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 09/15/2020] [Indexed: 12/11/2022] Open
Abstract
Gene expression analysis is emerging as a new diagnostic tool in transplant pathology, in particular for the diagnosis of antibody-mediated rejection. Diagnostic gene expression panels are defined on the basis of their pathophysiological relevance, but also need to be tested for their robustness across different preservatives and analysis platforms. The aim of this study is the investigate the effect of tissue sampling and preservation on candidate genes included in a renal transplant diagnostic panel. Using the NanoString platform, we compared the expression of 219 genes in 51 samples, split for formalin-fixation and paraffin-embedding (FFPE) and RNAlater preservation (RNAlater). We found that overall, gene expression significantly correlated between FFPE and RNAlater samples. However, at the individual gene level, 46 of the 219 genes did not correlate across the 51 matched FFPE and RNAlater samples. Comparing gene expression results using NanoString and qRT-PCR for 18 genes in the same pool of RNA (RNAlater), we found a significant correlation in 17/18 genes. Our study indicates that, in samples from the same routine diagnostic renal transplant biopsy procedure split for FFPE and RNAlater, 21% of 219 genes of potential biological significance do not correlate in expression. Whether this is due to fixatives or tissue sampling, selection of gene panels for routine diagnosis should take this information into consideration.
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Affiliation(s)
- F Toulza
- Department of Immunology and Inflammation, Centre for Inflammatory Diseases, Faculty of Medicine, Imperial College, London, UK
| | - K Dominy
- Molecular Pathology Laboratory, North West London Pathology, London, UK
| | - T Cook
- Department of Immunology and Inflammation, Centre for Inflammatory Diseases, Faculty of Medicine, Imperial College, London, UK
| | - J Galliford
- Imperial Kidney and Transplant Centre, London, UK
| | - J Beadle
- Department of Immunology and Inflammation, Centre for Inflammatory Diseases, Faculty of Medicine, Imperial College, London, UK
| | - A McLean
- Imperial Kidney and Transplant Centre, London, UK
| | - C Roufosse
- Department of Immunology and Inflammation, Centre for Inflammatory Diseases, Faculty of Medicine, Imperial College, London, UK.
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9
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Circulating Tumour DNAs and Non-Coding RNAs as Liquid Biopsies for the Management of Colorectal Cancer Patients. GASTROINTESTINAL DISORDERS 2020. [DOI: 10.3390/gidisord2030022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Circulating tumour DNAs and non-coding RNAs present in body fluids have been under investigation as tools for cancer diagnosis, disease monitoring, and prognosis for many years. These so-called liquid biopsies offer the opportunity to obtain information about the molecular make-up of a cancer in a minimal invasive way and offer the possibility to implement theranostics for precision oncology. Furthermore, liquid biopsies could overcome the limitations of tissue biopsies in capturing the complexity of tumour heterogeneity within the primary cancer and among different metastatic sites. Liquid biopsies may also be implemented to detect early tumour formation or to monitor cancer relapse of response to therapy with greater sensitivity compared with the currently available protein-based blood biomarkers. Most colorectal cancers are often diagnosed at late stages and have a high mortality rate. Hence, biomolecules as nucleic acids present in liquid biopsies might have prognostic potential and could serve as predictive biomarkers for chemotherapeutic regimens. This review will focus on the role of circulating tumour DNAs and non-coding RNAs as diagnostic, prognostic, and predictive biomarkers in the context of colorectal cancer.
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10
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Allison KH, Hammond MEH, Dowsett M, McKernin SE, Carey LA, Fitzgibbons PL, Hayes DF, Lakhani SR, Chavez-MacGregor M, Perlmutter J, Perou CM, Regan MM, Rimm DL, Symmans WF, Torlakovic EE, Varella L, Viale G, Weisberg TF, McShane LM, Wolff AC. Estrogen and Progesterone Receptor Testing in Breast Cancer: American Society of Clinical Oncology/College of American Pathologists Guideline Update. Arch Pathol Lab Med 2020; 144:545-563. [PMID: 31928354 DOI: 10.5858/arpa.2019-0904-sa] [Citation(s) in RCA: 180] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
PURPOSE.— To update key recommendations of the American Society of Clinical Oncology/College of American Pathologists estrogen receptor (ER) and progesterone receptor (PgR) testing in breast cancer guideline. METHODS.— A multidisciplinary international Expert Panel was convened to update the clinical practice guideline recommendations informed by a systematic review of the medical literature. RECOMMENDATIONS.— The Expert Panel continues to recommend ER testing of invasive breast cancers by validated immunohistochemistry as the standard for predicting which patients may benefit from endocrine therapy, and no other assays are recommended for this purpose. Breast cancer samples with 1% to 100% of tumor nuclei positive should be interpreted as ER positive. However, the Expert Panel acknowledges that there are limited data on endocrine therapy benefit for cancers with 1% to 10% of cells staining ER positive. Samples with these results should be reported using a new reporting category, ER Low Positive, with a recommended comment. A sample is considered ER negative if < 1% or 0% of tumor cell nuclei are immunoreactive. Additional strategies recommended to promote optimal performance, interpretation, and reporting of cases with an initial low to no ER staining result include establishing a laboratory-specific standard operating procedure describing additional steps used by the laboratory to confirm/adjudicate results. The status of controls should be reported for cases with 0% to 10% staining. Similar principles apply to PgR testing, which is used primarily for prognostic purposes in the setting of an ER-positive cancer. Testing of ductal carcinoma in situ (DCIS) for ER is recommended to determine potential benefit of endocrine therapies to reduce risk of future breast cancer, while testing DCIS for PgR is considered optional. Additional information can be found at www.asco.org/breast-cancer-guidelines .
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Affiliation(s)
| | | | | | | | | | | | | | - Sunil R Lakhani
- University of Queensland, Brisbane, Queensland, Australia
- Pathology Queensland, Brisbane, Queensland, Australia
| | | | | | | | - Meredith M Regan
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | | | | | - Emina E Torlakovic
- Saskatchewan Health Authority, Saskatoon, Saskatchewan, Canada
- University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | | | - Giuseppe Viale
- IEO, European Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico, Milan, Italy
- University of Milan, Milan, Italy
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11
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Allison KH, Hammond MEH, Dowsett M, McKernin SE, Carey LA, Fitzgibbons PL, Hayes DF, Lakhani SR, Chavez-MacGregor M, Perlmutter J, Perou CM, Regan MM, Rimm DL, Symmans WF, Torlakovic EE, Varella L, Viale G, Weisberg TF, McShane LM, Wolff AC. Estrogen and Progesterone Receptor Testing in Breast Cancer: ASCO/CAP Guideline Update. J Clin Oncol 2020; 38:1346-1366. [PMID: 31928404 DOI: 10.1200/jco.19.02309] [Citation(s) in RCA: 650] [Impact Index Per Article: 162.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2019] [Indexed: 12/13/2022] Open
Abstract
PURPOSE To update key recommendations of the American Society of Clinical Oncology/College of American Pathologists estrogen (ER) and progesterone receptor (PgR) testing in breast cancer guideline. METHODS A multidisciplinary international Expert Panel was convened to update the clinical practice guideline recommendations informed by a systematic review of the medical literature. RECOMMENDATIONS The Expert Panel continues to recommend ER testing of invasive breast cancers by validated immunohistochemistry as the standard for predicting which patients may benefit from endocrine therapy, and no other assays are recommended for this purpose. Breast cancer samples with 1% to 100% of tumor nuclei positive should be interpreted as ER positive. However, the Expert Panel acknowledges that there are limited data on endocrine therapy benefit for cancers with 1% to 10% of cells staining ER positive. Samples with these results should be reported using a new reporting category, ER Low Positive, with a recommended comment. A sample is considered ER negative if < 1% or 0% of tumor cell nuclei are immunoreactive. Additional strategies recommended to promote optimal performance, interpretation, and reporting of cases with an initial low to no ER staining result include establishing a laboratory-specific standard operating procedure describing additional steps used by the laboratory to confirm/adjudicate results. The status of controls should be reported for cases with 0% to 10% staining. Similar principles apply to PgR testing, which is used primarily for prognostic purposes in the setting of an ER-positive cancer. Testing of ductal carcinoma in situ (DCIS) for ER is recommended to determine potential benefit of endocrine therapies to reduce risk of future breast cancer, while testing DCIS for PgR is considered optional. Additional information can be found at www.asco.org/breast-cancer-guidelines.
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Affiliation(s)
| | | | | | | | | | | | | | - Sunil R Lakhani
- University of Queensland, Brisbane, Queensland, Australia
- Pathology Queensland, Brisbane, Queensland, Australia
| | | | | | | | - Meredith M Regan
- Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA
| | | | | | - Emina E Torlakovic
- Saskatchewan Health Authority, Saskatoon, Saskatchewan, Canada
- University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | | | - Giuseppe Viale
- IEO, European Institute of Oncology, Istituto di Ricovero e Cura a Carattere Scientifico, Milan, Italy
- University of Milan, Milan, Italy
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12
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Gu YY, Luo B, Li CY, Huang LS, Chen G, Feng ZB, Peng ZG. Expression and clinical significance of neuropilin-1 in Epstein-Barr virus-associated lymphomas. Cancer Biomark 2020; 25:259-273. [PMID: 31282408 DOI: 10.3233/cbm-192437] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
BACKGROUND The expression of neuropilin-1 (NRP-1) in Epstein-Barr virus (EBV)-associated lymphomas and its relationships with clinicopathological parameters was investigated. METHODS The researchers compared 111 cases of patients with lymphoma to 20 cases of reactive lymphoid hyperplasia. In situ hybridization was applied to observe the expression of EBV-encoded RNA (EBER) in lymphomas, and immunohistochemistry was used to detect the NRP-1 expression in lymphoma tissues and lymph node tissues with reactive hyperplasia. RESULTS In these 111 cases, the EBER of 62 cases (55.9%) appeared positive. NRP-1 was relatively highly expressed in lymphomas (P= 0.019). Further, NRP-1 showed higher expression in lymphomas with positive EBER than in negative ones. A comprehensive analysis revealed that NRP-1 was differently expressed in NK/T-cell lymphoma, Hodgkin's lymphoma, diffuse large B-cell lymphoma, and anaplastic large cell lymphoma (P= 0.027). Moreover, highly expressed NRP-1 was found to be a useful independent prognostic factor in assessing overall survival and progression-free survival rates in cases of non-Hodgkin's lymphoma (NHL). CONCLUSIONS NRP-1 exhibited higher expression in lymphomas, and it was positively expressed in EBV-positive lymphomas. Moreover, highly expressed NRP-1 can be used as an undesirable independent prognostic factor in NHL.
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Affiliation(s)
- Yong-Yao Gu
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China.,Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Bin Luo
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China.,Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Chun-Yao Li
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Lan-Shan Huang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Gang Chen
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Zhen-Bo Feng
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China
| | - Zhi-Gang Peng
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi 530021, China
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13
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Impact of the updated 2018 ASCO/CAP guidelines on HER2 FISH testing in invasive breast cancer: a retrospective study of HER2 fish results of 2233 cases. Breast Cancer Res Treat 2019; 175:51-57. [DOI: 10.1007/s10549-019-05148-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 01/22/2019] [Indexed: 12/18/2022]
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14
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Daull P, Barabino S, Feraille L, Kessal K, Docquier M, Parsadaniantz SM, Baudouin C, Garrigue JS. Modulation of Inflammation-Related Genes in the Cornea of a Mouse Model of Dry Eye upon Treatment with Cyclosporine Eye Drops. Curr Eye Res 2019; 44:476-485. [PMID: 30664361 DOI: 10.1080/02713683.2018.1563197] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Purpose/Aim: Inflammation is recognized as playing an etiological role in dry eye disease. This study aimed to assess the efficacy of various topical cyclosporine A (CsA) formulations on cornea inflammatory markers in a mouse model of dry eye. MATERIAL AND METHODS Six- to 7-week-old mice treated with scopolamine were housed in a controlled environment room to induce dry eye. Following dry eye confirmation by corneal fluorescein staining (CFS), the mice were treated three times a day with: 0.05%CsA (Restasis, Allergan), 0.1%CsA (Ikervis, Santen), 1%CsA oil solution, and 0.5% loteprednol etabonate (LE, Lotemax, Baush+Lomb), or left untreated. Aqueous tear production and CFS scores were assessed during the treatment period, and corneas were collected to measure the expression profile of a selection of inflammatory genes. RESULTS After 7 days of treatment, the CFS scores were reduced by 21%, 31%, and 44% with 0.05%CsA, 0.1%CsA, and 1%CsA eye drops, respectively. By contrast, 0.5% LE did not decrease corneal fluorescein staining at day 10. A statistically significant dose-dependent CFS reduction was observed only between the 0.05% and 1%CsA formulations. The gene expression profiles indicated that 12, 18, 17 genes were downregulated by 0.05%CsA, 0.1%CsA, 1%CsA, respectively. Among them, the genes significantly downregulated were: IL1A, IL1R1, and TLR4 with 0.05%CsA; H2-Eb1, IL1A, IL1B, IL1RN, IL6, TGFB2, TGFB3, TLR2, TLR3, and TLR4 with 0.1%CsA; IL1B, IL6, TGFB3, and TLR4 with 1%CsA. TGFB1 and TGFBR1 were the only genes upregulated in all groups, but only TGFB1 upregulation reached significance. IL6RA was significantly upregulated by 0.05%CsA. CONCLUSIONS This study indicates that the three CsA formulations effectively modulated TLR4, TGFβ1, IL1, and IL6 pathways to reduce corneal epithelium lesions in a mouse model of severe dry eye. The study also suggests that the different anti-inflammatory eye drops modulated inflammatory genes in a slightly different manner.
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Affiliation(s)
- Philippe Daull
- a Novagali Innovation Center , SANTEN SAS, Novagali Innovation Center , Evry Cedex , France
| | - Stefano Barabino
- b Ocular Surface & Dry Eye Center, Ospedale L. Sacco, University of Milan , Milan , Italy
| | - Laurence Feraille
- c Iris Pharma, Les Nertières, Allée Hector Pintus , La Gaude , France
| | - Karima Kessal
- d Vision Institute UMR S 968, UMR 7210 CNRS, Paris Sorbonne Universités , Paris , France
| | - Mylene Docquier
- e iGE3 , University of Geneva Medical School , Geneva 4 , Switzerland
| | | | - Christophe Baudouin
- d Vision Institute UMR S 968, UMR 7210 CNRS, Paris Sorbonne Universités , Paris , France.,f CHNO XV-XX Hospital , Paris , France
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