1
|
Immunophenotypic and molecular characterization of pancreatic neuroendocrine tumors producing serotonin. Mod Pathol 2022; 35:1713-1722. [PMID: 35739266 DOI: 10.1038/s41379-022-01110-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 05/12/2022] [Accepted: 05/12/2022] [Indexed: 11/08/2022]
Abstract
Serotonin producing pancreatic neuroendocrine tumors (SP-PanNET) account for 0.58-1.4% of all pancreatic neuroendocrine tumors (PanNET). They may present with atypical symptoms, such as acute pancreatitis and are often radiologically characterized by main pancreatic duct dilatation. SP-PanNET are well differentiated neuroendocrine tumors (NET) distinct from classical PanNET by atypical serotonin secretion and abundant dense stroma deposition, like serotonin producing ileal NET leading in some cases to difficulties to reliably distinguish SP-PanNET from ileal NET metastases. The biology and molecular profile of SP-PanNET remain poorly characterized and the cell of origin within the pancreas is unclear. To address these questions, we analyzed a large cohort of SP-PanNET by immunohistochemistry (n = 29; ATRX, DAXX, MENIN, Islet1, PAX6, PDX1, ARX, CDX2), whole genome copy number array (Oncoscan™) and a large NGS panel (NovoPM™) (n = 10), FISH (n = 13) and RNA sequencing (n = 24) together with 21 ileal NET and 29 nonfunctioning PanNET (NF-PanNET). These analyses revealed a unique genomic profile with frequent isolated loss of chromosome 1 (14 cases-61%) and few pathogenic mutations (KMT2C in 2 cases, ARID1A in 1 case). Unsupervised RNAseq-based clustering showed that SP-PanNET were closer to NF-PanNET than ileal NET with an exclusive beta cell-like signature. SP-PanNET showed TGF-β pathway activation signatures associated with extracellular matrix remodeling and similar signature were reproduced in vitro when pancreatic stellate cells were exposed to serotonin. SP-PanNET immunohistochemical profile resemble that of ileal NET except for PDX1 and PAX6 expression to a lesser extend suggesting that these two markers may be useful to diagnose SP-PanNET. Taken together, this suggests that SP-PanNET are a very specific PanNET entity with a peculiar biology leading to the characteristic fibrotic aspect.
Collapse
|
2
|
Schmitt F, Di Lorito A, Vielh P. Molecular Testing on Cytology for Gene Fusion Detection. Front Med (Lausanne) 2021; 8:643113. [PMID: 34295907 PMCID: PMC8289888 DOI: 10.3389/fmed.2021.643113] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 05/31/2021] [Indexed: 12/26/2022] Open
Abstract
Cytology samples are suitable for the study of genotypic and phenotypic changes observed in different tumors. Being a minimally invasive technique, cytology sampling has been used as an acceptable alternative to track the alterations associated with tumor progression. Although the detection of gene mutations is well-established on cytology, in the last few years, gene fusion detections are becoming mandatory, especially in some tumor types such as lung cancer. Different technologies are available such as immunocytochemistry, fluorescence in situ hybridization, reverse transcription-polymerase chain reaction, and massive parallel sequencing approaches. Considering that many new drugs targeted fusion proteins, cytological samples can be of use to detect gene fusions in solid and lymphoproliferative tumor patients. In this article, we revised the use of several techniques utilized to check gene fusions in cytological material.
Collapse
Affiliation(s)
- Fernando Schmitt
- Medical Faculty of Porto University, Porto, Portugal.,Unit of Molecular Pathology of Institute of Molecular Pathology and Immunology of University of Porto, Porto, Portugal.,CIntesis@RISE, Porto, Portugal
| | | | | |
Collapse
|
3
|
Cros J, Théou-Anton N, Gounant V, Nicolle R, Reyes C, Humez S, Hescot S, Thomas de Montpréville V, Guyétant S, Scoazec JY, Guyard A, de Mestier L, Brosseau S, Mordant P, Castier Y, Gentien D, Ruszniewski P, Zalcman G, Couvelard A, Cazes A. Specific Genomic Alterations in High-Grade Pulmonary Neuroendocrine Tumours with Carcinoid Morphology. Neuroendocrinology 2021; 111:158-169. [PMID: 32015233 DOI: 10.1159/000506292] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 01/30/2020] [Indexed: 11/19/2022]
Abstract
INTRODUCTION High-grade lung neuroendocrine tumours with carcinoid morphology have been recently reported; they may represent the thoracic counterparts of grade 3 digestive neuroendocrine tumours. We aimed to study their genetic landscape including analysis of tumoral heterogeneity. METHODS Eleven patients with high-grade (>20% Ki-67 and/or >10 mitoses) lung neuroendocrine tumours with a carcinoid morphology were included. We analysed copy number variations, somatic mutations, and protein expression in 16 tumour samples (2 samples were available for 5 patients allowing us to study spatial and temporal heterogeneity). RESULTS Genomic patterns were heterogeneous ranging from "quiet" to tetraploid, heavily rearranged genomes. Oncogene mutations were rare and most genetic alterations targeted tumour suppressor genes. Chromosomes 11 (7/11), 3 (6/11), 13 (4/11), and 6-17 (3/11) were the most frequently lost. Altered tumour suppressor genes were common to both carcinoids and neuroendocrine carcinomas, involving different pathways including chromatin remodelling (KMT2A, ARID1A, SETD2, SMARCA2, BAP1, PBRM1, KAT6A), DNA repair (MEN1, POLQ, ATR, MLH1, ATM), cell cycle (RB1, TP53, CDKN2A), cell adhesion (LATS2, CTNNB1, GSK3B) and metabolism (VHL). Comparative spatial/temporal analyses confirmed that these tumours emerged from clones of lower aggressivity but revealed that they were genetically heterogeneous accumulating "neuroendocrine carcinoma-like" genetic alterations through progression such as TP53/RB1 alterations. CONCLUSION These data confirm the importance of chromatin remodelling genes in pulmonary carcinoids and highlight the potential role of TP53 and RB1 to drive the transformation in more aggressive high-grade tumours.
Collapse
Affiliation(s)
- Jerôme Cros
- Department of Pathology, ENETS Centre of Excellence, Beaujon-Bichat Hospitals, AP-HP, Paris, France
- Université de Paris, Paris, France
- INSERM U1149, Centre de Recherche sur l'Inflammation, Paris, France
| | | | - Valérie Gounant
- Department of Thoracic Oncology and Early Phase Clinical Trials Unit (CIC1425/CLIP2), Bichat Hospital, AP-HP, Paris, France
| | - Remy Nicolle
- Programme Cartes d'Identité des Tumeurs (CIT), Ligue Nationale Contre le Cancer, Paris, France
| | - Cécile Reyes
- Institut Curie, PSL Research University, Translational Research Department, Genomics Platform, Paris, France
| | - Sarah Humez
- Department of Pathology, CHRU de Lille, Lille, France
| | - Ségolène Hescot
- Department of Nuclear Medicine, Institut Curie, CLCC, Saint-Cloud, France
| | | | | | - Jean-Yves Scoazec
- Department of Biopathology, Gustave Roussy Cancer Campus, Villejuif, France
- Faculté de Médecine, Université Paris Saclay, Le Kremlin-Bicêtre, France
| | - Alice Guyard
- Department of Pathology, ENETS Centre of Excellence, Beaujon-Bichat Hospitals, AP-HP, Paris, France
| | - Louis de Mestier
- Université de Paris, Paris, France
- INSERM U1149, Centre de Recherche sur l'Inflammation, Paris, France
- Department of Gastroenterology and Pancreatology, Beaujon Hospital, AP-HP, Clichy, France
| | - Solenn Brosseau
- Université de Paris, Paris, France
- Department of Thoracic Oncology and Early Phase Clinical Trials Unit (CIC1425/CLIP2), Bichat Hospital, AP-HP, Paris, France
| | - Pierre Mordant
- Université de Paris, Paris, France
- Department of Vascular and Thoracic Surgery, Bichat University Hospital, AP-HP, Université de Paris, Paris, France
| | - Yves Castier
- Université de Paris, Paris, France
- Department of Vascular and Thoracic Surgery, Bichat University Hospital, AP-HP, Université de Paris, Paris, France
| | - David Gentien
- Institut Curie, PSL Research University, Translational Research Department, Genomics Platform, Paris, France
| | - Philippe Ruszniewski
- Université de Paris, Paris, France
- INSERM U1149, Centre de Recherche sur l'Inflammation, Paris, France
- Department of Gastroenterology and Pancreatology, Beaujon Hospital, AP-HP, Clichy, France
| | - Gérard Zalcman
- Université de Paris, Paris, France
- Department of Thoracic Oncology and Early Phase Clinical Trials Unit (CIC1425/CLIP2), Bichat Hospital, AP-HP, Paris, France
| | - Anne Couvelard
- Department of Pathology, ENETS Centre of Excellence, Beaujon-Bichat Hospitals, AP-HP, Paris, France,
- Université de Paris, Paris, France,
- INSERM U1149, Centre de Recherche sur l'Inflammation, Paris, France,
| | - Aurélie Cazes
- Department of Pathology, ENETS Centre of Excellence, Beaujon-Bichat Hospitals, AP-HP, Paris, France
- Université de Paris, Paris, France
- INSERM U1152, Paris, France
| |
Collapse
|
4
|
Gentien D, Piqueret-Stephan L, Henry E, Albaud B, Rapinat A, Koscielny S, Scoazec JY, Vielh P. Digital Multiplexed Gene Expression Analysis of mRNA and miRNA from Routinely Processed and Stained Cytological Smears: A Proof-of-Principle Study. Acta Cytol 2020; 65:88-98. [PMID: 33011718 DOI: 10.1159/000510174] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 07/14/2020] [Indexed: 12/20/2022]
Abstract
OBJECTIVE Although transcriptomic assessments of small samples using high-throughput techniques are usually performed on fresh or frozen tissues, there is a growing demand for those performed on stained cellular specimens already used for diagnostic purposes. STUDY DESIGN The possibility of detecting mRNAs and microRNAs (miRNAs) from routinely processed cytological samples using nCounter® technology was explored. Fresh samples from pleural and peritoneal effusions were analyzed using 2 parallel methods: samples were smeared and routinely stained using the May-Grünwald-Giemsa or Diff-Quik® method and mounted using conventional methods, and they were also studied following a snap freezing method, in which samples were maintained at -80°C until use. mRNAs and miRNAs were assessed and compared after total RNA extraction from both routinely processed samples and their matched frozen controls. RESULTS A good concordance was found between the gene expression measured in routinely processed samples and their matched frozen controls for the majority of mRNAs and miRNAs tested. However, the standard deviation of low-expressed miRNA was high. CONCLUSIONS Although nCounter® technology is a robust method to measure and characterize both mRNAs and miRNAs from routinely processed cytological samples, caution is recommended for the interpretation of low-expressed miRNA.
Collapse
Affiliation(s)
- David Gentien
- Translational Research Department, Genomics Platform, Institut Curie, PSL Research University, Paris, France
| | - Laure Piqueret-Stephan
- INSERM UMR 981, Villejuif, France
- Translational Research Laboratory, AMMICa (CNRS UMS3655, INSERM US23, Paris Sud University) Gustave Roussy, Villejuif, France
| | - Emilie Henry
- Translational Research Department, Genomics Platform, Institut Curie, PSL Research University, Paris, France
| | - Benoît Albaud
- Translational Research Department, Genomics Platform, Institut Curie, PSL Research University, Paris, France
| | - Audrey Rapinat
- Translational Research Department, Genomics Platform, Institut Curie, PSL Research University, Paris, France
| | - Serge Koscielny
- Department of Biostatistics, Gustave Roussy, Villejuif, France
| | - Jean-Yves Scoazec
- Translational Research Laboratory, AMMICa (CNRS UMS3655, INSERM US23, Paris Sud University) Gustave Roussy, Villejuif, France
- Department of Medical Biology and Pathology, Gustave Roussy, Villejuif, France
| | - Philippe Vielh
- INSERM UMR 981, Villejuif, France,
- Translational Research Laboratory, AMMICa (CNRS UMS3655, INSERM US23, Paris Sud University) Gustave Roussy, Villejuif, France,
- Department of Medical Biology and Pathology, Gustave Roussy, Villejuif, France,
| |
Collapse
|
5
|
Bourrier C, Pierga JY, Xuereb L, Salaun H, Proudhon C, Speicher MR, Belic J, Heitzer E, Lockhart BP, Guigal-Stephan N. Shallow Whole-Genome Sequencing from Plasma Identifies FGFR1 Amplified Breast Cancers and Predicts Overall Survival. Cancers (Basel) 2020; 12:cancers12061481. [PMID: 32517171 PMCID: PMC7353062 DOI: 10.3390/cancers12061481] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/26/2020] [Accepted: 06/04/2020] [Indexed: 12/30/2022] Open
Abstract
Background: Focal amplification of fibroblast growth factor receptor 1 (FGFR1) defines a subgroup of breast cancers with poor prognosis and high risk of recurrence. We sought to demonstrate the potential of circulating cell-free DNA (cfDNA) analysis to evaluate FGFR1 copy numbers from a cohort of 100 metastatic breast cancer (mBC) patients. Methods: Formalin-fixed paraffin-embedded (FFPE) tissue samples were screened for FGFR1 amplification by FISH, and positive cases were confirmed with a microarray platform (OncoscanTM). Subsequently, cfDNA was evaluated by two approaches, i.e., mFAST-SeqS and shallow whole-genome sequencing (sWGS), to estimate the circulating tumor DNA (ctDNA) allele fraction (AF) and to evaluate the FGFR1 status. Results: Tissue-based analyses identified FGFR1 amplifications in 20/100 tumors. All cases with a ctDNA AF above 3% (n = 12) showed concordance for FGFR1 status between tissue and cfDNA. In one case, we were able to detect a high-level FGFR1 amplification, although the ctDNA AF was below 1%. Furthermore, high levels of ctDNA indicated an association with unfavorable prognosis based on overall survival. Conclusions: Screening for FGFR1 amplification in ctDNA might represent a viable strategy to identify patients eligible for treatment by FGFR inhibition, and mBC ctDNA levels might be used for the evaluation of prognosis in clinical drug trials.
Collapse
Affiliation(s)
- Chantal Bourrier
- Division of Biotechnology, Servier Research Institute, 125, Chemin de ronde, 78290 Croissy Sur-seine, France; (C.B.); (B.P.L.)
| | - Jean-Yves Pierga
- Department of Medical Oncology, Institut Curie, 26 rue d’Ulm, 75005 Paris, France; (J.-Y.P.); (H.S.)
- Circulating Tumor Biomarkers Laboratory, Institut Curie, PSL Research University, INSERM CIC 1428, 26 rue d’Ulm, 75005 Paris, France;
- Université de Paris, 75005 Paris, France
| | - Laura Xuereb
- Division of Methodology and Valorisation of Data, Servier Research and Development Institute, 50 rue carnot, 92150 Suresnes, France;
| | - Hélène Salaun
- Department of Medical Oncology, Institut Curie, 26 rue d’Ulm, 75005 Paris, France; (J.-Y.P.); (H.S.)
- Université de Paris, 75005 Paris, France
| | - Charlotte Proudhon
- Circulating Tumor Biomarkers Laboratory, Institut Curie, PSL Research University, INSERM CIC 1428, 26 rue d’Ulm, 75005 Paris, France;
| | - Michael R. Speicher
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; (M.R.S.); (J.B.); (E.H.)
- BioTechMed-Graz, 8010 Graz, Austria
| | - Jelena Belic
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; (M.R.S.); (J.B.); (E.H.)
| | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic and Research Center for Molecular BioMedicine, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria; (M.R.S.); (J.B.); (E.H.)
- BioTechMed-Graz, 8010 Graz, Austria
- Christian Doppler Laboratory for Liquid Biopsies for Early Detection of Cancer, 8010 Graz, Austria
| | - Brian Paul Lockhart
- Division of Biotechnology, Servier Research Institute, 125, Chemin de ronde, 78290 Croissy Sur-seine, France; (C.B.); (B.P.L.)
| | - Nolwen Guigal-Stephan
- Division of Biotechnology, Servier Research Institute, 125, Chemin de ronde, 78290 Croissy Sur-seine, France; (C.B.); (B.P.L.)
- Correspondence: ; Tel.: +33-155-722-532
| |
Collapse
|
6
|
Pote A, Boghenco O, Marques-Ramos A. Molecular analysis of H&E- and Papanicolau-stained samples-systematic review. Histochem Cell Biol 2020; 154:7-20. [PMID: 32372108 DOI: 10.1007/s00418-020-01882-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2020] [Indexed: 12/12/2022]
Abstract
Molecular pathology allows the identification of causative agents in infectious diseases and detection of biomarkers important for prediction of disease susceptibility, diagnosis and personalized therapy. Accordingly, nucleic acid-based methods have gained a special role in clinical laboratories particularly to evaluate solid and hematological tumors. Extraction of nucleic acids is commonly performed in microdissected formalin-fixed paraffin-embedded (FFPE) or cytological samples that had been previously evaluated through the use of hematoxylin and eosin (H&E) or Papanicolau (Pap) stains, respectively. Although the effect of both stains on nucleic acids integrity has been explored by several authors, the results are not consistent and require further examination. Accordingly, the goal of this review was to assess the influence of H&E and Pap stains on DNA and RNA integrity and to address the mechanism by which each staining compromises molecular based-analysis. The analyzed studies demonstrate that H&E- and Pap-staining result in low DNA recovery and some degree of DNA fragmentation. Additionally, it is concluded that hemalum inhibits PCR by interfering with DNA extraction, preventing DNA polymerase attachment and possibly by rescuing divalent cations. Accordingly, proper sample purification and adjustment of PCR conditions are of key importance to achieve satisfactory results by PCR in H&E- and Pap-stained samples. Furthermore, although H&E results in RNA fragmentation, it is possible to perform expression analysis in H&E-stained frozen sections, using RNase-free conditions, low amounts of hematoxylin and a rapid protocol from sample collection to RNA analysis. It The effect of Pap-staining on RNA integrity remains to be determined.
Collapse
Affiliation(s)
- Alexandra Pote
- ESTeSL, Escola Superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, Av. D. João II, Lote 4.69.01, 1990-096, Lisboa, Portugal
| | - Otília Boghenco
- ESTeSL, Escola Superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, Av. D. João II, Lote 4.69.01, 1990-096, Lisboa, Portugal
| | - Ana Marques-Ramos
- ESTeSL, Escola Superior de Tecnologia da Saúde de Lisboa, Instituto Politécnico de Lisboa, Av. D. João II, Lote 4.69.01, 1990-096, Lisboa, Portugal.
- H&TRC, Health and Technology Research Center, ESTeSL-Escola Superior de Tecnologia da Saúde, Instituto Politécnico de Lisboa, Lisboa, Portugal.
| |
Collapse
|
7
|
Pisapia P, Malapelle U, Roma G, Saddar S, Zheng Q, Pepe F, Bruzzese D, Vigliar E, Bellevicine C, Luthra R, Nikiforov YE, Mayo-de-Las-Casas C, Molina-Vila MA, Rosell R, Bihl M, Savic S, Bubendorf L, de Biase D, Tallini G, Hwang DH, Sholl LM, Vander Borght S, Weynand B, Stieber D, Vielh P, Rappa A, Barberis M, Fassan M, Rugge M, De Andrea CE, Lozano MD, Lupi C, Fontanini G, Schmitt F, Dumur CI, Bisig B, Bongiovanni M, Merkelbach-Bruse S, Büttner R, Nikiforova MN, Roy-Chowdhuri S, Troncone G. Consistency and reproducibility of next-generation sequencing in cytopathology: A second worldwide ring trial study on improved cytological molecular reference specimens. Cancer Cytopathol 2019; 127:285-296. [PMID: 31021538 DOI: 10.1002/cncy.22134] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 03/05/2019] [Accepted: 04/02/2019] [Indexed: 02/05/2023]
Abstract
BACKGROUND Artificial genomic reference standards in a cytocentrifuge/cytospin format with well-annotated genomic data are useful for validating next-generation sequencing (NGS) on routine cytopreparations. Here, reference standards were optimized to be stained by different laboratories before DNA extraction and to contain a lower number of cells (2 × 105 ). This was done to better reflect the clinical challenge of working with insufficient cytological material. METHODS A total of 17 worldwide laboratories analyzed customized reference standard slides (slides A-D). Each laboratory applied its standard workflow. The sample slides were engineered to harbor epidermal growth factor receptor (EGFR) c.2235_2249del15 p.E746_A750delELREA, EGFR c.2369C>T p.T790M, Kirsten rat sarcoma viral oncogene homolog (KRAS) c.38G>A p.G13D, and B-Raf proto-oncogene, serine/threonine kinase (BRAF) c.1798_1799GT>AA p.V600K mutations at various allele frequencies (AFs). RESULTS EGFR and KRAS mutation detection showed excellent interlaboratory reproducibility, especially on slides A and B (10% and 5% AFs). On slide C (1% AF), either the EGFR mutation or the KRAS mutation was undetected by 10 of the 17 laboratories (58.82%). A reassessment of the raw data in a second-look analysis highlighted the mutations (n = 10) that had been missed in the first-look analysis. BRAF c.1798_1799GT>AA p.V600K showed a lower concordance rate for mutation detection and AF quantification. CONCLUSIONS The data show that the detection of low-abundance mutations is still clinically challenging and may require a visual inspection of sequencing reads to detect. Genomic reference standards in a cytocentrifuge/cytospin format are a valid tool for regular quality assessment of laboratories performing molecular studies on cytology with low-AF mutations.
Collapse
Affiliation(s)
- Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Gianluca Roma
- AccuRef Diagnostics, Applied Stem Cell, Inc, Milpitas, California
| | - Sonika Saddar
- AccuRef Diagnostics, Applied Stem Cell, Inc, Milpitas, California
| | - Qi Zheng
- AccuRef Diagnostics, Applied Stem Cell, Inc, Milpitas, California
| | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Dario Bruzzese
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Elena Vigliar
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Claudio Bellevicine
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Rajyalakshmi Luthra
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yuri E Nikiforov
- Department of Pathology and Laboratory Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | | | | | - Rafael Rosell
- Catalan Institute of Oncology, Badalona, Spain
- Rosell Cancer Institute, Quiròn-Dexeus University Institute, Barcelona, Spain
| | - Michel Bihl
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Spasenija Savic
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Lukas Bubendorf
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Dario de Biase
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Giovanni Tallini
- Anatomic Pathology, University of Bologna Medical Center, Bologna, Italy
| | - David H Hwang
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | | | - Birgit Weynand
- Department of Pathology, University Hospitals Leuven, Leuven, Belgium
| | | | | | - Alessandra Rappa
- Division of Pathology, European Institute of Oncology, Milan, Italy
| | - Massimo Barberis
- Division of Pathology, European Institute of Oncology, Milan, Italy
| | - Matteo Fassan
- Surgical Pathology Unit, Department of Medicine, University of Padua, Padua, Italy
| | - Massimo Rugge
- Surgical Pathology Unit, Department of Medicine, University of Padua, Padua, Italy
| | | | - Maria D Lozano
- Department of Pathology, University Clinic of Navarra, Pamplona, Spain
| | - Cristiana Lupi
- Department of Surgical, Medical, and Molecular Pathology and Critical Area, University of Pisa, Pisa, Italy
| | - Gabriella Fontanini
- Department of Surgical, Medical, and Molecular Pathology and Critical Area, University of Pisa, Pisa, Italy
| | - Fernando Schmitt
- Institute of Molecular Pathology and Immunology, University of Porto, Porto, Portugal
- Department of Pathology, Medical Faculty, Porto University, Porto, Portugal
| | - Catherine I Dumur
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia
| | - Bettina Bisig
- Institute of Pathology, Lausanne University Hospital, Lausanne, Switzerland
| | | | - Sabine Merkelbach-Bruse
- Institute of Pathology and Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Reinhard Büttner
- Institute of Pathology and Center for Molecular Medicine, University of Cologne, Cologne, Germany
| | - Marina N Nikiforova
- Department of Pathology and Laboratory Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Sinchita Roy-Chowdhuri
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | | |
Collapse
|
8
|
Sanchez A, Bocklage T. Precision cytopathology: expanding opportunities for biomarker testing in cytopathology. J Am Soc Cytopathol 2019; 8:95-115. [PMID: 31287426 DOI: 10.1016/j.jasc.2018.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 12/14/2018] [Accepted: 12/15/2018] [Indexed: 06/09/2023]
Abstract
Precision cytopathology refers to therapeutically linked biomarker testing in cytopatology, a dynamically growing area of the discipline. This review describes basic steps to expand precision cytopathology services. Focusing exclusively on solid tumors, the review is divided into four sections: Section 1: Overview of precision pathology- opportunities and challenges; Section 2: Basic steps in establishing or expanding a precision cytopathology laboratory; Section 3: Cytopathology specimens suitable for next generation sequencing platforms; and Section 4: Summary. precision cytopathology continues to rapidly evolve in parallel with expanding targeted therapy options. Biomarker assays (companion diagnostics) comprise a multitude of test types including immunohistochemistry, in situ hybridization and molecular genetic tests such as PCR and next generation sequencing all of which are performable on cytology specimens. Best practices for precision cytopathology will incorporate traditional diagnostic approaches allied with careful specimen triage to enable successful biomarker analysis. Beyond triaging, cytopathologists knowledgeable about molecular test options and capabilities have the opportunity to refine diagnoses, prognoses and predictive information thereby assuming a lead role in precision oncology biomarker testing.
Collapse
Affiliation(s)
| | - Thèrése Bocklage
- Department of Pathology and Laboratory Medicine, University of Kentucky College of Medicine, MS.
| |
Collapse
|
9
|
Lozano MD, Echeveste JI, Abengozar M, Mejías LD, Idoate MA, Calvo A, de Andrea CE. Cytology Smears in the Era of Molecular Biomarkers in Non-Small Cell Lung Cancer: Doing More With Less. Arch Pathol Lab Med 2019; 142:291-298. [PMID: 29494220 DOI: 10.5858/arpa.2017-0208-ra] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT - The rapid advances in targeted therapies in non-small cell lung cancer (NSCLC) make the optimization and implementation of cytology specimens for molecular testing a priority. Up to 70% of patients with NSCLC are diagnosed at advanced stages and tissue biopsies often cannot be taken. Although cytology samples provide high-quality material for molecular testing, molecular cytopathology is not yet well known or widely used. OBJECTIVE - To report the many advances in molecular cytopathology and the suitability and utility of cytology samples in molecular and genetic testing of NSCLC. DATA SOURCES - Data sources comprised published peer-reviewed literature and personal experience of the authors. CONCLUSIONS - Molecular testing can be performed on cytologic specimens, especially on direct smears. Rapid on-site evaluation by cytopathologists has improved the adequacy and the management of cytology samples for molecular testing. Mutational profiling of NSCLC using next-generation sequencing can be performed on cytology samples from very small amounts of DNA. Fluorescence in situ hybridization assays on cytology specimens, including stained direct smear, offer some distinct advantages over their histologic counterpart, and are used to detect ALK and ROS1 rearrangements in NSCLC. Cytology specimens allow assessment of the entire tumor cell nucleus, avoiding signal loss from truncation artifacts. The use of cytology samples for assessing programmed death ligand-1 protein expression is currently being developed. Protocols for bisulfite conversion and DNA droplet digital polymerase chain reaction assays have been optimized for cytology smear to investigate aberrant DNA methylation of several NSCLC-related genes.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Carlos E de Andrea
- From the Department of Pathology, Clínica Universidad de Navarra, (Drs Lozano, Echeveste, Abengozar, Mejías, Idoate, and de Andrea), IDISNA and Program in Solid Tumors and Biomarkers, Center for Applied Medical Research (CIMA) (Dr Calvo), and the Department of Histology and Pathology (Drs Calvo and de Andrea), University of Navarra, Pamplona, Spain
| |
Collapse
|
10
|
Mito JK, Conner JR, Hornick JL, Cibas ES, Qian X. SOX10/keratin dual-color immunohistochemistry: An effective first-line test for the workup of epithelioid malignant neoplasms in FNA and small biopsy specimens. Cancer Cytopathol 2018; 126:179-189. [DOI: 10.1002/cncy.21960] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 11/18/2017] [Accepted: 12/01/2017] [Indexed: 12/12/2022]
Affiliation(s)
- Jeffrey K. Mito
- Department of Pathology; Brigham and Women's Hospital, and Harvard Medical School; Boston Massachusetts
| | - James R. Conner
- Department of Pathology; Brigham and Women's Hospital, and Harvard Medical School; Boston Massachusetts
| | - Jason L. Hornick
- Department of Pathology; Brigham and Women's Hospital, and Harvard Medical School; Boston Massachusetts
| | - Edmund S. Cibas
- Department of Pathology; Brigham and Women's Hospital, and Harvard Medical School; Boston Massachusetts
| | - Xiaohua Qian
- Department of Pathology; Brigham and Women's Hospital, and Harvard Medical School; Boston Massachusetts
| |
Collapse
|
11
|
Leichsenring J, Volckmar AL, Kirchner M, Kazdal D, Kriegsmann M, Stögbauer F, Bockmayr T, Klauschen F, Herth FJF, Penzel R, Warth A, Schirmacher P, Endris V, Stenzinger A. Targeted deep sequencing of effusion cytology samples is feasible, informs spatiotemporal tumor evolution, and has clinical and diagnostic utility. Genes Chromosomes Cancer 2017; 57:70-79. [PMID: 29044880 DOI: 10.1002/gcc.22509] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 10/05/2017] [Accepted: 10/11/2017] [Indexed: 12/12/2022] Open
Abstract
During the course of disease, many cancer patients eventually present with metastatic disease including peritoneal or pleural spread. In this context, cytology specimens derived from ascites or pleural effusion may help to differentiate malignant from benign conditions and sometimes yield diagnosis of a malignancy. However, even when supported by immunohistochemistry, cytological interpretation can be challenging, especially if tumor cellularity is low. Here, we investigated whether targeted deep sequencing of formalin-fixed and paraffin embedded (FFPE) cytology specimens of cancer patients is feasible, and has diagnostic and clinical impact. To this end, a cohort of 20 matched pairs was compiled, each comprising a cytology sample (FFPE cell block) and at least one biopsy/surgical resection specimen serving as benchmark. In addition, 5 non-malignant effusions were sequenced serving as negative-controls. All samples yielded sufficient libraries and were successfully subjected to targeted sequencing employing a semiconductor based next-generation sequencing platform. Using gene panels of different size and composition, including the Oncomine Comprehensive Assay, for targeted sequencing, somatic mutations were detected in the tissue of all 20 cases. Of these, 15 (75%) harbored mutations that were also detected in the corresponding cytology samples. In four of these cases (20%), additional private mutations were detected in either cytology or tissue samples, reflecting spatiotemporal tumor evolution. Of the five remaining cases, three (15%) showed wild type alleles in cytology material whereas tumor tissue had mutations in interrogated genes. Two cases were discordant, showing different private mutations in the cytology and in the tissue sample, respectively. In summary, sequencing of cytology specimens (FFPE cell block) reflecting spatiotemporal tumor evolution is feasible and yields adjunct genetic information that may be exploitable for diagnostics and therapy.
Collapse
Affiliation(s)
- Jonas Leichsenring
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Anna-Lena Volckmar
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Martina Kirchner
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Daniel Kazdal
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Mark Kriegsmann
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Fabian Stögbauer
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Teresa Bockmayr
- Institute of Pathology, Charité University Hospital, Berlin, Germany
| | | | - Felix J F Herth
- Department of Pneumology and Critical Care Medicine, Thoraxklinik at University Hospital Heidelberg, Heidelberg, Germany.,Translational Lung Research Center Heidelberg, German Center for Lung Research (DZL), Heidelberg, Germany
| | - Roland Penzel
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Arne Warth
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Translational Lung Research Center Heidelberg, German Center for Lung Research (DZL), Heidelberg, Germany
| | - Peter Schirmacher
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,German Cancer Consortium (DKTK), Partner Site Heidelberg, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Volker Endris
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Albrecht Stenzinger
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,German Cancer Consortium (DKTK), Partner Site Heidelberg, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| |
Collapse
|
12
|
Malapelle U, Mayo-de-Las-Casas C, Molina-Vila MA, Rosell R, Savic S, Bihl M, Bubendorf L, Salto-Tellez M, de Biase D, Tallini G, Hwang DH, Sholl LM, Luthra R, Weynand B, Vander Borght S, Missiaglia E, Bongiovanni M, Stieber D, Vielh P, Schmitt F, Rappa A, Barberis M, Pepe F, Pisapia P, Serra N, Vigliar E, Bellevicine C, Fassan M, Rugge M, de Andrea CE, Lozano MD, Basolo F, Fontanini G, Nikiforov YE, Kamel-Reid S, da Cunha Santos G, Nikiforova MN, Roy-Chowdhuri S, Troncone G. Consistency and reproducibility of next-generation sequencing and other multigene mutational assays: A worldwide ring trial study on quantitative cytological molecular reference specimens. Cancer Cytopathol 2017; 125:615-626. [PMID: 28475299 DOI: 10.1002/cncy.21868] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 02/23/2017] [Accepted: 03/10/2017] [Indexed: 02/05/2023]
Abstract
BACKGROUND Molecular testing of cytological lung cancer specimens includes, beyond epidermal growth factor receptor (EGFR), emerging predictive/prognostic genomic biomarkers such as Kirsten rat sarcoma viral oncogene homolog (KRAS), neuroblastoma RAS viral [v-ras] oncogene homolog (NRAS), B-Raf proto-oncogene, serine/threonine kinase (BRAF), and phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit α (PIK3CA). Next-generation sequencing (NGS) and other multigene mutational assays are suitable for cytological specimens, including smears. However, the current literature reflects single-institution studies rather than multicenter experiences. METHODS Quantitative cytological molecular reference slides were produced with cell lines designed to harbor concurrent mutations in the EGFR, KRAS, NRAS, BRAF, and PIK3CA genes at various allelic ratios, including low allele frequencies (AFs; 1%). This interlaboratory ring trial study included 14 institutions across the world that performed multigene mutational assays, from tissue extraction to data analysis, on these reference slides, with each laboratory using its own mutation analysis platform and methodology. RESULTS All laboratories using NGS (n = 11) successfully detected the study's set of mutations with minimal variations in the means and standard errors of variant fractions at dilution points of 10% (P = .171) and 5% (P = .063) despite the use of different sequencing platforms (Illumina, Ion Torrent/Proton, and Roche). However, when mutations at a low AF of 1% were analyzed, the concordance of the NGS results was low, and this reflected the use of different thresholds for variant calling among the institutions. In contrast, laboratories using matrix-assisted laser desorption/ionization-time of flight (n = 2) showed lower concordance in terms of mutation detection and mutant AF quantification. CONCLUSIONS Quantitative molecular reference slides are a useful tool for monitoring the performance of different multigene mutational assays, and this could lead to better standardization of molecular cytopathology procedures. Cancer Cytopathol 2017;125:615-26. © 2017 American Cancer Society.
Collapse
Affiliation(s)
- Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | | | | | - Rafael Rosell
- Catalan Institute of Oncology, Badalona, Spain
- Instituto Oncológico Dr Rosell (IOR), Quirón-Dexeus University Institute, Barcelona, Spain
| | - Spasenija Savic
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Michel Bihl
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Lukas Bubendorf
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Manuel Salto-Tellez
- Molecular Pathology Programme, Centre for Cancer Research and Cell Biology Queen's University Belfast, Belfast, United Kingdom
| | - Dario de Biase
- Department of Pharmacy and Biotechnology - University of Bologna, Bologna, Italy
| | | | - David H Hwang
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts
| | - Rajyalakshmi Luthra
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Birgit Weynand
- Department of Pathology, Universitair Ziekenhuis Leuven, Leuven, Belgium
| | - Sara Vander Borght
- Department of Pathology, Universitair Ziekenhuis Leuven, Leuven, Belgium
| | - Edoardo Missiaglia
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Massimo Bongiovanni
- Institute of Pathology, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | | | | | | | - Alessandra Rappa
- Division of Pathology, European Institute of Oncology, Milan, Italy
| | - Massimo Barberis
- Division of Pathology, European Institute of Oncology, Milan, Italy
| | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Pasquale Pisapia
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Nicola Serra
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Elena Vigliar
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Claudio Bellevicine
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Matteo Fassan
- Department of Medicine (DIMED), Surgical Pathology Unit University of Padua, Padua, Italy
| | - Massimo Rugge
- Department of Medicine (DIMED), Surgical Pathology Unit University of Padua, Padua, Italy
| | | | - Maria D Lozano
- Department of Pathology, University Clinic of Navarra, Pamplona, Spain
| | - Fulvio Basolo
- Department of Surgical, Medical and Molecular Pathology and Critical Area, University of Pisa, Pisa, Italy
| | - Gabriella Fontanini
- Department of Surgical, Medical and Molecular Pathology and Critical Area, University of Pisa, Pisa, Italy
| | - Yuri E Nikiforov
- Department of Pathology and Laboratory Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Suzanne Kamel-Reid
- Department of Laboratory Medicine and Pathobiology, University Health Network, Toronto, Ontario, Canada
| | - Gilda da Cunha Santos
- Department of Laboratory Medicine and Pathobiology, University Health Network, Toronto, Ontario, Canada
| | - Marina N Nikiforova
- Department of Pathology and Laboratory Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Sinchita Roy-Chowdhuri
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Giancarlo Troncone
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | | |
Collapse
|
13
|
Pitman MB. Cancer Cytopathology: 20 years of advancing the field of pancreaticobiliary cytopathology. Cancer Cytopathol 2016; 124:690-694. [PMID: 27740727 DOI: 10.1002/cncy.21773] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 08/16/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Martha Bishop Pitman
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts.
| |
Collapse
|