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Evans M, Kendall T. Practical considerations for pathological diagnosis and molecular profiling of cholangiocarcinoma: an expert review for best practices. Expert Rev Mol Diagn 2024; 24:393-408. [PMID: 38752560 DOI: 10.1080/14737159.2024.2353696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024]
Abstract
INTRODUCTION Advances in precision medicine have expanded access to targeted therapies and demand for molecular profiling of cholangiocarcinoma (CCA) patients in routine clinical practice. However, pathologists face challenges in establishing a definitive intrahepatic CCA (iCCA) diagnosis while preserving sufficient tissue for molecular profiling. Additionally, they frequently face challenges in optimal tissue handling to preserve nucleic acid integrity. AREAS COVERED This article first identifies the challenges in establishing a definitive diagnosis of iCCA in a lesional liver biopsy while preserving sufficient tissue for molecular profiling. Then, the authors explore the clinical value of molecular profiling, the basic principles of single gene and next-generation sequencing (NGS) techniques, and the challenges in tissue sampling for genomic testing. They also propose an algorithm for best practice in tissue management for molecular profiling of CCA. EXPERT OPINION Several practical challenges face pathologists during tissue sampling and processing for molecular profiling. Optimized tissue processing, careful tissue handling, and selection of appropriate approaches to molecular testing are essential to ensure that the highest possible quality of diagnostic information is provided in the greatest proportion of cases.
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Affiliation(s)
- Matt Evans
- Cellular Pathologist, University Hospital Southampton NHS Foundation Trust, Southampton, UK
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2
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Solomon JP. Practical Considerations for Oncogenic Fusion Detection and Reporting in Solid Tumors. J Appl Lab Med 2024; 9:116-123. [PMID: 38167769 DOI: 10.1093/jalm/jfad068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/15/2023] [Indexed: 01/05/2024]
Abstract
BACKGROUND Chromosomal rearrangements that result in oncogenic fusions can hold tremendous clinical significance in solid tumors, often with diagnostic or treatment implications. CONTENT Traditionally, low-throughput methods such as fluorescence in situ hybridization were used to identify fusions in the clinical laboratory. With the rise of next-generation sequencing techniques and the broad adoption of comprehensive genomic profiling, the practice of screening for fusions as part of an oncologic workup has evolved. RNA sequencing methods are increasingly used, as these comprehensive high-throughput assays have many advantages over traditional techniques. Several RNA sequencing platforms are available, each with benefits and drawbacks. Regardless of the approach, systematic evaluation of the RNA sequencing results and the fusions identified by the assay should be performed. Assessment of fusion events relies upon evaluation of quality evidence, structural evidence, and functional evidence to ensure accurate fusion reporting and interpretation. SUMMARY Given the clinical significance of gene fusions in oncology, understanding the variety of assays available for fusion detection, their benefits and drawbacks, and how they are used in the identification and interpretation of gene fusions is important for the modern precision oncology practice.
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Affiliation(s)
- James P Solomon
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, United States
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3
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von der Thüsen J. Thymic epithelial tumours: histopathological classification and differential diagnosis. Histopathology 2024; 84:196-215. [PMID: 37994555 DOI: 10.1111/his.15097] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023]
Abstract
The epithelial and lymphoid compartments of the thymus can give rise to a wide variety of tumours, including thymomas, thymic carcinomas, lymphoreticular proliferations, germ cell tumours, and sarcomas. While some of these have close similarity to their counterparts in other organs, both in terms of histology and immunohistochemistry, as well as molecular features, others are unique to the thymus. The epithelial tumours, which can develop in the thymus, will be discussed in this review, with a particular emphasis on resolving differential diagnosis by means of morphology, immunohistochemical profiles, and molecular diagnostics.
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Affiliation(s)
- Jan von der Thüsen
- Department of Pathology and Clinical Bioinformatics, Erasmus MC, Rotterdam, The Netherlands
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4
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Wu S, Liu Y, Li K, Liang Z, Zeng X. Molecular and cytogenetic features of NTRK fusions enriched in BRAF and RET double-negative papillary thyroid cancer. J Mol Diagn 2023:S1525-1578(23)00106-X. [PMID: 37236546 DOI: 10.1016/j.jmoldx.2023.04.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 02/17/2023] [Accepted: 04/10/2023] [Indexed: 05/28/2023] Open
Abstract
Rare NTRK-driven malignant neoplasms can be effectively inhibited by anti-TRK agents. The discovery of NTRK1/2/3-rich tumours in papillary thyroid cancer (PTC) patients is a precondition for the rapid identification of NTRK fusion tumours. Knowledge of NTRK gene activation is critical to accurately detect NTRK status. A total of 229 BRAF V600E-negative samples from PTC patients were analysed in this study. Break-apart fluorescence in situ hybridisation (FISH) was performed to detect RET fusion. NTRK status was analysed using FISH, DNA- and RNA-based next-generation sequencing (NGS), and quantitative reverse transcription-polymerase chain reaction (RT-qPCR). In 128 BRAF and RET double-negative cases, 56 (43.8%, 56/128) NTRK rearrangement tumours were found, including 1 NTRK2, 16 NTRK1, and 39 NTRK3 fusions. Two novel NTRK fusions, EZR::NTRK1 and EML4::NTRK2, was found in the NTRK rearrangement tumors.Dominant break-apart and extra 3' signal patterns accounted for 89.3% (50/56) and 5.4% (3/56) of all NTRK-positive cases, respectively, as determined by FISH. In our cohort, there were 2.3% (3/128) FISH false-negative and 3.1% (4/128) FISH false-positive cases identified. NTRK fusions are highly recurrent in BRAF and RET double-negative PTCs. FISH or RNA-based NGS is a reliable detection approach. NTRK rearrangement can be precisely, rapidly, and economically detected based on the developed optimal algorithm.
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Affiliation(s)
- Shafei Wu
- Department of Pathology, Peking Union Medical College Hospital, and Molecular Pathology Research Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Yuanyuan Liu
- Department of Pathology, Peking Union Medical College Hospital, and Molecular Pathology Research Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Kaimi Li
- Department of Pathology, Peking Union Medical College Hospital, and Molecular Pathology Research Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Zhiyong Liang
- Department of Pathology, Peking Union Medical College Hospital, and Molecular Pathology Research Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China.
| | - Xuan Zeng
- Department of Pathology, Peking Union Medical College Hospital, and Molecular Pathology Research Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China.
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5
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van Gulik AL, Sluydts E, Vervoort L, Kockx M, Kortman P, Ylstra B, Finn SP, Bubendorf L, Bahce I, Sie D, Radonic T, Lissenberg-Witte B, Thunnissen E. False positivity in break apart fluorescence in-situ hybridization due to polyploidy. Transl Lung Cancer Res 2023; 12:676-688. [PMID: 37197629 PMCID: PMC10183404 DOI: 10.21037/tlcr-22-516] [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: 07/12/2022] [Accepted: 03/08/2023] [Indexed: 05/19/2023]
Abstract
Background In-situ hybridization (ISH) is a diagnostic tool in the detection of chromosomal anomalies, which has important implications for diagnosis, classification and prediction of cancer therapy in various diseases. Certain thresholds of number of cells showing an aberrant pattern are commonly used to declare a sample as positive for genomic rearrangements. The phenomenon of polyploidy can be misleading in the interpretation of break apart fluorescence in-situ hybridization (FISH). The aim of this study is to investigate the impact of cell size and ploidy on FISH results. Methods In sections of varying thickness of control liver tissue and non-small cell lung cancer cases, nuclear size was measured and the number of MET chromogenic ISH and ALK FISH (liver) or ALK and ROS1 FISH (lung cancer) signals was manually counted and quantified. Results In liver cell nuclei the number of FISH/chromogenic ISH signals increases with nuclear size related to physiological polyploidy and is related to section thickness. In non-small cell lung cancer cases tumour cells with higher ploidy levels and nuclear size have an increased chance of single signals. Furthermore, additional lung cancer samples with borderline ALK FISH results were examined with a commercial kit for rearrangements. No rearrangements could be demonstrated, proving a false positive ALK FISH result. Conclusions In case of polyploidy there is an increased likelihood of false positivity when using break apart FISH probes. Therefore, we state that prescribing one single cut-off in FISH is inappropriate. In polyploidy, the currently proposed cut-off should only be used with caution and the result should be confirmed by an additional technique.
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Affiliation(s)
| | | | | | | | - Pim Kortman
- Department of Pathology, Amsterdam University Medical Center, Location VUmc, Amsterdam, The Netherlands
| | - Bauke Ylstra
- Department of Pathology, Amsterdam University Medical Center, Location VUmc, Amsterdam, The Netherlands
| | - Stephen P. Finn
- University of Dublin, Trinity College and St. James’s Hospital, Dublin, Ireland
| | - Lukas Bubendorf
- Institute of Pathology, University Hospital Basel, Basel, Switzerland
| | - Idris Bahce
- Department of Pulmonology, Amsterdam University Medical Center, Location VUmc, Amsterdam, The Netherlands
| | - Daoud Sie
- Amsterdam University Medical Center, Location VUmc, Tumor Genome Analysis Core, Amsterdam, The Netherlands
| | - Teodora Radonic
- Department of Pathology, Amsterdam University Medical Center, Location VUmc, Amsterdam, The Netherlands
| | - Birgit Lissenberg-Witte
- Department of Epidemiology and Data Science, Amsterdam University Medical Center, Location VUmc, Amsterdam, The Netherlands
| | - Erik Thunnissen
- Department of Pathology, Amsterdam University Medical Center, Location VUmc, Amsterdam, The Netherlands
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6
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Sorokin M, Rabushko E, Rozenberg JM, Mohammad T, Seryakov A, Sekacheva M, Buzdin A. Clinically relevant fusion oncogenes: detection and practical implications. Ther Adv Med Oncol 2022; 14:17588359221144108. [PMID: 36601633 PMCID: PMC9806411 DOI: 10.1177/17588359221144108] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 11/22/2022] [Indexed: 12/28/2022] Open
Abstract
Mechanistically, chimeric genes result from DNA rearrangements and include parts of preexisting normal genes combined at the genomic junction site. Some rearranged genes encode pathological proteins with altered molecular functions. Those which can aberrantly promote carcinogenesis are called fusion oncogenes. Their formation is not a rare event in human cancers, and many of them were documented in numerous study reports and in specific databases. They may have various molecular peculiarities like increased stability of an oncogenic part, self-activation of tyrosine kinase receptor moiety, and altered transcriptional regulation activities. Currently, tens of low molecular mass inhibitors are approved in cancers as the drugs targeting receptor tyrosine kinase (RTK) oncogenic fusion proteins, that is, including ALK, ABL, EGFR, FGFR1-3, NTRK1-3, MET, RET, ROS1 moieties. Therein, the presence of the respective RTK fusion in the cancer genome is the diagnostic biomarker for drug prescription. However, identification of such fusion oncogenes is challenging as the breakpoint may arise in multiple sites within the gene, and the exact fusion partner is generally unknown. There is no gold standard method for RTK fusion detection, and many alternative experimental techniques are employed nowadays to solve this issue. Among them, RNA-seq-based methods offer an advantage of unbiased high-throughput analysis of only transcribed RTK fusion genes, and of simultaneous finding both fusion partners in a single RNA-seq read. Here we focus on current knowledge of biology and clinical aspects of RTK fusion genes, related databases, and laboratory detection methods.
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Affiliation(s)
| | - Elizaveta Rabushko
- Moscow Institute of Physics and Technology,
Dolgoprudny, Moscow Region, Russia,I.M. Sechenov First Moscow State Medical
University, Moscow, Russia
| | | | - Tharaa Mohammad
- Moscow Institute of Physics and Technology,
Dolgoprudny, Moscow Region, Russia
| | | | - Marina Sekacheva
- I.M. Sechenov First Moscow State Medical
University, Moscow, Russia
| | - Anton Buzdin
- Moscow Institute of Physics and Technology,
Dolgoprudny, Moscow Region, Russia,I.M. Sechenov First Moscow State Medical
University, Moscow, Russia,Shemyakin-Ovchinnikov Institute of Bioorganic
Chemistry, Moscow, Russia,PathoBiology Group, European Organization for
Research and Treatment of Cancer (EORTC), Brussels, Belgium
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7
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Hu B, Sajid M, Lv R, Liu L, Sun C. A review of spatial profiling technologies for characterizing the tumor microenvironment in immuno-oncology. Front Immunol 2022; 13:996721. [PMID: 36389765 PMCID: PMC9659855 DOI: 10.3389/fimmu.2022.996721] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/17/2022] [Indexed: 08/13/2023] Open
Abstract
Interpreting the mechanisms and principles that govern gene activity and how these genes work according to -their cellular distribution in organisms has profound implications for cancer research. The latest technological advancements, such as imaging-based approaches and next-generation single-cell sequencing technologies, have established a platform for spatial transcriptomics to systematically quantify the expression of all or most genes in the entire tumor microenvironment and explore an array of disease milieus, particularly in tumors. Spatial profiling technologies permit the study of transcriptional activity at the spatial or single-cell level. This multidimensional classification of the transcriptomic and proteomic signatures of tumors, especially the associated immune and stromal cells, facilitates evaluation of tumor heterogeneity, details of the evolutionary trajectory of each tumor, and multifaceted interactions between each tumor cell and its microenvironment. Therefore, spatial profiling technologies may provide abundant and high-resolution information required for the description of clinical-related features in immuno-oncology. From this perspective, the present review will highlight the importance of spatial transcriptomic and spatial proteomics analysis along with the joint use of other sequencing technologies and their implications in cancers and immune-oncology. In the near future, advances in spatial profiling technologies will undoubtedly expand our understanding of tumor biology and highlight possible precision therapeutic targets for cancer patients.
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Affiliation(s)
- Bian Hu
- Department of Hepatobiliary Surgery, Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Transplant and Immunology Laboratory, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Muhammad Sajid
- Department of Hepatobiliary Surgery, Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Transplant and Immunology Laboratory, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Rong Lv
- Blood Transfusion Laboratory, Anhui Blood Center, Hefei, China
| | - Lianxin Liu
- Department of Hepatobiliary Surgery, Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Cheng Sun
- Department of Hepatobiliary Surgery, Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Transplant and Immunology Laboratory, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Chinese Academy of Sciences (CAS) Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Institute of Immunology, University of Science and Technology of China, Hefei, China
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8
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Wang SS, Wang F, Zeng Z, Gao F, Liu HH, Wang HN, Hu Y, Qin HF. Case Report: A novel intergenic MIR4299/MIR8070-RET fusion with RET amplification and clinical response to pralsetinib in a lung adenocarcinoma patient. Front Oncol 2022; 12:929763. [PMID: 36226049 PMCID: PMC9548572 DOI: 10.3389/fonc.2022.929763] [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: 05/03/2022] [Accepted: 09/02/2022] [Indexed: 12/31/2022] Open
Abstract
The identification of receptor-tyrosine kinase gene (RET) fusions in lung cancer has become crucial owing to actionable events that predict responsiveness to tyrosine kinase inhibitors (TKIs). However, RET fusions with distinct partner genes respond differently to TKIs. In this case, a 60-year-old man was diagnosed with advanced lung adenocarcinoma. A novel RET-MIR4299/MIR8070 fusion and RET amplification were identified using next-generation sequencing (NGS). The patient was then administered with pralsetinib. After 3 weeks of therapy, the patient had a partial response. At the time of reporting, the patient was on continuous pralsetinib. These findings broaden the range of RET fusion types and provide the basis for the hypothesis that RET intergenic fusion and amplification respond to pralsetinib treatment in lung adenocarcinoma.
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Affiliation(s)
- Sha-Sha Wang
- Department of Oncology, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Fang Wang
- Department of Internal Medicine, OASIS International Hospital, Beijing, China
| | - Zhen Zeng
- Department of Oncology, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Fang Gao
- Department of Oncology, Chinese People's Liberation Army General Hospital, Beijing, China
| | - Huan-Huan Liu
- Department of Medicine, Acornmed Biotechnology Co., Ltd., Beijing, China
| | - Hui-Na Wang
- Department of Medicine, Acornmed Biotechnology Co., Ltd., Beijing, China
| | - Yi Hu
- Department of Oncology, Chinese People's Liberation Army General Hospital, Beijing, China,*Correspondence: Hai-Feng Qin, ; Yi Hu,
| | - Hai-Feng Qin
- Department of Oncology, Chinese People's Liberation Army General Hospital, Beijing, China,*Correspondence: Hai-Feng Qin, ; Yi Hu,
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9
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Caliò A, Cheng L, Martignoni G, Zhang S, Brunelli M, Eble JN. Mixed epithelial and stromal tumours of the kidney with malignant transformation: a clinicopathological study of four cases. Pathology 2022; 54:707-720. [PMID: 35697534 DOI: 10.1016/j.pathol.2022.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 03/02/2022] [Accepted: 03/10/2022] [Indexed: 11/18/2022]
Abstract
Mixed epithelial and stromal tumour of the kidney is a complex benign neoplasm in which malignancy rarely arises. In this study, we report four mixed epithelial and stromal tumours in which sarcoma or carcinoma developed. In the first, a multifocal adenocarcinoma arose and areas of transition from benign to malignant epithelium were observed. Oestrogen and progesterone receptors were diffusely present in the nuclei of the spindle cell stroma of the benign component. The second was a sarcoma in which benign epithelial elements were intermixed. Outside the renal parenchyma, clusters of small benign glands surrounded by oestrogen receptor-positive benign stroma were present, supporting the diagnosis of mixed epithelial and stromal tumour. Fluorescence in situ hybridisation for SYT-SSX translocation and immunohistochemical results, specifically TLE1 -ativity, argued against primary renal synovial sarcoma. The patient died 24 months after surgery. The third tumour consisted of small blue round cells, positive for epithelial membrane antigen, BCL2, CD99, and FLI1. Throughout the tumour, the presence of benign appearing branching tubules in fibromuscular stroma, reactive for smooth muscle actin, desmin and progesterone receptor, supported the diagnosis of mixed epithelial and stromal tumour in which a small round blue cell sarcoma with EWSR1 rearrangement arose. In the fourth tumour, adenocarcinoma with papillary architecture arose in a typical mixed epithelial and stromal tumour. In summary, we present four cases of mixed epithelial and stromal tumour with malignant transformation, two showing carcinomatous and the other two with sarcomatous transformation. Identification of typical benign looking elements and the absence of SYT-SSX translocation are helpful in recognition of this entity.
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Affiliation(s)
- Anna Caliò
- Department of Diagnostic and Public Health, Section of Pathology, University of Verona, Verona, Italy; Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Liang Cheng
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Urology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Guido Martignoni
- Department of Diagnostic and Public Health, Section of Pathology, University of Verona, Verona, Italy
| | - Shaobo Zhang
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Matteo Brunelli
- Department of Diagnostic and Public Health, Section of Pathology, University of Verona, Verona, Italy
| | - John N Eble
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.
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10
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Yu Q, Zhang C, Huang W, Li L. Heat-induced antigen retrieval in fluorescence in situ hybridization: An effective approach enhancing signal intensity in poor-quality FFPE sections. Exp Ther Med 2021; 22:1480. [PMID: 34765021 PMCID: PMC8576618 DOI: 10.3892/etm.2021.10915] [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: 07/01/2021] [Accepted: 09/17/2021] [Indexed: 11/06/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) serves as an ancillary tool for assessing chromosomal abnormalities and is important in differential diagnoses and treatment decisions. In clinical practice, pathologists encounter unsatisfactory formalin-fixed paraffin-embedded (FFPE) sections exhibiting weak fluorescence signals, mostly due to inappropriate tissue processing or preservation, leading to interpretation difficulties. For the present study, FFPE samples for which conventional FISH failed were collected. Instead of a pretreatment step using a commercial kit, heat-induced antigen retrieval (HIAR) was introduced using either citrate buffer or Tris-EDTA buffer, while the subsequent experimental workflow remained unchanged. After HIAR-assisted FISH, the hybridization efficiency and signal intensity were markedly enhanced and no difference in signal adequacy was observed when comparing the effect of the two AR solutions. The present study demonstrated that HIAR is a reliable tool for FISH, particularly for poor-quality FFPE sections yielding weak or no fluorescence signals in the conventional analysis.
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Affiliation(s)
- Qiuxiao Yu
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, Guangdong 518116, P.R. China
| | - Chi Zhang
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, Guangdong 518116, P.R. China
| | - Wenting Huang
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, Guangdong 518116, P.R. China
| | - Li Li
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, Guangdong 518116, P.R. China
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11
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Aref-Eshghi E, Lin F, Li MM, Zhong Y. The oncogenic roles of NTRK fusions and methods of molecular diagnosis. Cancer Genet 2021; 258-259:110-119. [PMID: 34710798 DOI: 10.1016/j.cancergen.2021.10.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 09/23/2021] [Accepted: 10/16/2021] [Indexed: 10/20/2022]
Abstract
The NTRK gene family is composed of NTRK1, NTRK2, and NTRK3, which encode three tropomyosin-receptor kinases, belonging to a class of tyrosine kinase receptors. These proteins are known to play roles in cell proliferation, differentiation, apoptosis, and survival. Fusions involving the NTRK genes are long known as drivers in many tumors. Although they occur in less than 5% of all malignancies, their occurrence in a great diversity of tumors has been documented. Several rare tumors including infantile fibrosarcoma, secretory breast carcinoma, and mammary analogue secretory carcinoma are accompanied by NTRK fusions in more than 90% of cases, demonstrating a diagnostic value for the NTRK fusion testing in these tumors. More recently, the development of effective targeted therapies has created a demand for their detection in all malignancies. A variety of approaches are available for testing including immunohistochemistry, fluorescence in situ hybridization (FISH), reverse transcription polymerase chain reaction (RT-PCR), and DNA- and RNA-based next-generation sequencing (NGS). This article reviews the molecular biology and tumorigenesis of NTRK fusions, their prevalence and clinical significance with a focus on available methods for fusion detection. The advantages and limitations of different technologies, the best practice algorithms for NTRK fusion detection, and the future direction of NTRK testing are also discussed.
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Affiliation(s)
- Erfan Aref-Eshghi
- Department of Pathology and Laboratory Medicine, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Fumin Lin
- Department of Pathology and Laboratory Medicine, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Marilyn M Li
- Department of Pathology and Laboratory Medicine, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States; Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA, United States
| | - Yiming Zhong
- Department of Pathology and Laboratory Medicine, Division of Genomic Diagnostics, Children's Hospital of Philadelphia, Philadelphia, PA, United States; Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States.
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12
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Liehr T. Molecular Cytogenetics in the Era of Chromosomics and Cytogenomic Approaches. Front Genet 2021; 12:720507. [PMID: 34721522 PMCID: PMC8548727 DOI: 10.3389/fgene.2021.720507] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 09/22/2021] [Indexed: 02/04/2023] Open
Abstract
Here the role of molecular cytogenetics in the context of yet available all other cytogenomic approaches is discussed. A short introduction how cytogenetics and molecular cytogenetics were established is followed by technical aspects of fluorescence in situ hybridization (FISH). The latter contains the methodology itself, the types of probe- and target-DNA, as well as probe sets. The main part deals with examples of modern FISH-applications, highlighting unique possibilities of the approach, like the possibility to study individual cells and even individual chromosomes. Different variants of FISH can be used to retrieve information on genomes from (almost) base pair to whole genomic level, as besides only second and third generation sequencing approaches can do. Here especially highlighted variations of FISH are molecular combing, chromosome orientation-FISH (CO-FISH), telomere-FISH, parental origin determination FISH (POD-FISH), FISH to resolve the nuclear architecture, multicolor-FISH (mFISH) approaches, among other applied in chromoanagenesis studies, Comet-FISH, and CRISPR-mediated FISH-applications. Overall, molecular cytogenetics is far from being outdated and actively involved in up-to-date diagnostics and research.
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Affiliation(s)
- Thomas Liehr
- Jena University Hospital, Institute of Human Genetics, Friedrich Schiller University, Jena, Germany
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13
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da Cunha IW, de Almeida Coudry R, de Macedo MP, de Assis EACP, Stefani S, Soares FA. A call to action: molecular pathology in Brazil. SURGICAL AND EXPERIMENTAL PATHOLOGY 2021. [DOI: 10.1186/s42047-021-00096-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Abstract
Background
Adoption of molecular pathology in Brazil is currently very limited. Of note, there are no programs for training new molecular pathologists in the country; thus, documents compiling nationally applicable information on molecular pathology are few.
Methods
A selected panel of Brazilian experts in fields related to molecular pathology were provided with a series of relevant questions to address prior to the multi-day conference. Within this conference, each narrative was discussed and edited by the entire group, through numerous drafts and rounds of discussion until a consensus was achieved.
Results
The panel proposes specific and realistic recommendations for implementing molecular pathology in cancer care in Brazil. In creating these recommendations, the authors strived to address all barriers to the widespread use and impediments to access mentioned previously within this manuscript.
Conclusion
This manuscript provides a review of molecular pathology principles as well as the current state of molecular pathology in Brazil. Additionally, the panel proposes practical and actionable recommendations for the implementation of molecular pathology throughout the country in order to increase awareness of the importance molecular pathology in Brazil.
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14
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Al-Obaidy KI, Bridge JA, Cheng L, Sumegi J, Reuter VE, Benayed R, Hameed M, Williamson SR, Hes O, Alruwaii FI, Segal JP, Wanjari P, Idrees MT, Nassiri M, Eble JN, Grignon DJ. EWSR1-PATZ1 fusion renal cell carcinoma: a recurrent gene fusion characterizing thyroid-like follicular renal cell carcinoma. Mod Pathol 2021; 34:1921-1934. [PMID: 34099871 DOI: 10.1038/s41379-021-00833-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 05/12/2021] [Accepted: 05/12/2021] [Indexed: 02/07/2023]
Abstract
Thyroid-like follicular renal cell carcinoma is an uncommon kidney tumor with no distinct molecular alteration described to date. This cohort of eight women with mean and median ages of 45 and 46 years, respectively (range 19-65 years), had unencapsulated, well-circumscribed tumors composed of tightly packed anastomosing follicle-like cysts filled with eosinophilic colloid-like material and lined by cuboidal cells with high nuclear to cytoplasmic ratios, oval to elongated nuclei with perpendicular arrangement toward the lumens, and prominent nuclear overlapping. The stroma between these was minimal with the exception of two tumors. Calcifications and necrosis were absent. Immunohistochemically, the tumors were positive for KRT19 (7/7), PAX8 (5/5), cyclin D1 (6/6), KRT7 (5/7), and AMACR (1/5; focal, weak), and were negative for WT1, TTF1 (transcription termination factor-1), and thyroglobulin. In three of three tumors tested molecularly, EWSR1-PATZ1 fusion was identified by RNA sequencing and confirmed by RT-PCR and Sanger sequencing. Over a follow-up period of 1-7 years, no evidence of recurrence or metastasis has been detected. The EWSR1-PATZ1 fusion has been recognized as a recurrent alteration in a subset of round to spindle cell sarcomas with EWSR1-non-ETS fusions (EWSR1-PATZ1 sarcoma) and in several central nervous system tumors. The finding of an EWSR1-PATZ1 fusion in all three of the thyroid-like follicular renal cell carcinomas for which sufficient tissue was available for genomic profiling provides the first distinct molecular abnormality in thyroid-like follicular renal cell carcinomas, supporting its designation as a distinct diagnostic entity.
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Affiliation(s)
- Khaleel I Al-Obaidy
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Julia A Bridge
- Division of Molecular Pathology, ProPath, Dallas, TX, USA.,Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Liang Cheng
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Janos Sumegi
- The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Victor E Reuter
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Meera Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Ondrej Hes
- Department of Pathology, Charles University Hospital Pilsen, Pilsen, Czech Republic
| | - Fatimah I Alruwaii
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Jeremy P Segal
- Department of Pathology, University of Chicago Medical Center, Chicago, IL, USA
| | - Pankhuri Wanjari
- Department of Pathology, University of Chicago Medical Center, Chicago, IL, USA
| | - Muhammad T Idrees
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Mehdi Nassiri
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - John N Eble
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - David J Grignon
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
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15
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Bishop JA, Koduru P, Veremis BM, Oliai BR, Weinreb I, Rooper LM, Dickson BC, Demicco EG. SS18 Break-Apart Fluorescence In Situ Hybridization is a Practical and Effective Method for Diagnosing Microsecretory Adenocarcinoma of Salivary Glands. Head Neck Pathol 2021; 15:723-726. [PMID: 33394377 PMCID: PMC8385014 DOI: 10.1007/s12105-020-01280-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/15/2020] [Accepted: 12/17/2020] [Indexed: 01/27/2023]
Abstract
Molecular analysis has allowed for refinement of salivary gland tumor classification and, in some cases, the recognition of entirely new tumor types. Microsecretory adenocarcinoma (MSA) is a salivary gland tumor described in 2019 characterized by microcystic growth, bland cytomorphology, luminal secretions, fibromyxoid stroma, and S100/p63 positivity with negative p40. Most important, MSA is defined by MEF2C-SS18 fusion. While this fusion has, to this point, been detected by next-generation sequencing, this is a technique that is currently inaccessible in most diagnostic laboratories. On the other hand, SS18 break-apart fluorescence in situ hybridization (FISH) is widely available and frequently used as an adjunct for diagnosing synovial sarcoma. It is not known if SS18 break-apart FISH is positive in tumors with MEF2C-SS18, or if it is entirely specific for MSA. Break apart FISH for SS18 was performed on 4 cases of MSA, as well as 8 tissue microarrays (TMAs) containing 423 various salivary gland carcinomas: 26 acinic cell carcinomas, 35 adenocarcinomas not otherwise specified, 96 adenoid cystic carcinomas, 3 basal cell adenocarcinomas, 20 epithelial-myoepithelial carcinomas, 15 hyalinizing clear cell carcinomas, 3 intraductal carcinomas, 12 myoepithelial carcinomas, 117 mucoepidermoid carcinomas, 30 polymorphous adenocarcinomas, 45 salivary duct carcinomas, 19 secretory carcinomas, and 2 undifferentiated carcinomas. SS18 break-apart FISH was also performed on whole slides of 2 tumors from the TMAs. All MSA cases demonstrated classic split patterns on SS18 break-apart FISH. On the TMAs, 374 cases were evaluable by FISH, and 372 cases were clearly negative for SS18 rearrangement. Two cases, both mucoepidermoid carcinomas, had rare split signals below the positivity threshold of 12% on their TMA cores, so FISH was performed on whole sections. On the whole sections both tumors were unequivocally negative for SS18 rearrangement. Taken together, SS18 break-apart FISH was 100% sensitive and 100% specific for a diagnosis of MSA. SS18 break-apart FISH, a diagnostic tool widely available in pathology laboratories, appears to be a highly accurate method for diagnosing MSA of salivary glands. Accordingly, this new tumor type may be molecularly confirmed without needing to resort to highly specialized techniques like next-generation sequencing.
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Affiliation(s)
- Justin A. Bishop
- Department of Pathology, University of Texas Southwestern Medical Center, Clements University Hospital UH04.250, 6201 Harry Hines Blvd., Dallas, TX 75390 USA ,Department of Pathology & Laboratory Medicine, Mount Sinai Hospital, Toronto, ON Canada
| | - Prasad Koduru
- Department of Pathology, University of Texas Southwestern Medical Center, Clements University Hospital UH04.250, 6201 Harry Hines Blvd., Dallas, TX 75390 USA
| | | | | | - Ilan Weinreb
- Department of Pathology, University Health Network, Toronto, ON Canada ,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada
| | - Lisa M. Rooper
- Department of Pathology, The Johns Hopkins Hospital, Baltimore, MD USA
| | - Brendan C. Dickson
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada ,Department of Pathology & Laboratory Medicine, Mount Sinai Hospital, Toronto, ON Canada
| | - Elizabeth G. Demicco
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON Canada ,Department of Pathology & Laboratory Medicine, Mount Sinai Hospital, Toronto, ON Canada
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16
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Cheng L, Davidson DD, Montironi R, Wang M, Lopez-Beltran A, Masterson TA, Albany C, Zhang S. Fluorescence In Situ Hybridization (FISH) Detection of Chromosomal 12p Anomalies in Testicular Germ Cell Tumors. Methods Mol Biol 2021; 2195:49-63. [PMID: 32852756 DOI: 10.1007/978-1-0716-0860-9_4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Gains of genetic material or internal rearrangements of chromosome 12p, including 12p overrepresentation or isochromosome 12p [i(12p)], are observed in virtually all germ cell tumors (GCT), in all histologic subtypes, and from various body locations. The chromosomal region involved in these alterations contains the growth and survival promoting oncogene KRAS (12p12.1). Gains or rearrangements of 12p characterize GCT from in situ to chemoresistant stages. Fluorescence in situ hybridization (FISH) detection of chromosome 12p anomalies is a sensitive and specific test for the diagnosis of germ cell tumors. Here we provide a detailed protocol for FISH detection of isochromosome 12p and chromosome 12p overrepresentation. The method is helpful for diagnosis of germ cell origin, and for selection of patients who may benefit from cisplatin-based chemotherapy.
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Affiliation(s)
- Liang Cheng
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.
- Department of Urology, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Darrell D Davidson
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Rodolfo Montironi
- Institute of Pathological Anatomy and Histopathology, School of Medicine, Polytechnic University of the Marche Region (Ancona), United Hospitals, Ancona, Italy
| | - Mingsheng Wang
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Antonio Lopez-Beltran
- Department of Pathology and Surgery, Faculty of Medicine, University of Cordoba, Cordoba, Spain
| | - Timothy A Masterson
- Department of Urology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Costantine Albany
- Department of Medicine, Division of Hematology and Oncology, Indiana University Simon Cancer Center, Indianapolis, IN, USA
| | - Shaobo Zhang
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
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17
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De Luca A, Esposito Abate R, Rachiglio AM, Maiello MR, Esposito C, Schettino C, Izzo F, Nasti G, Normanno N. FGFR Fusions in Cancer: From Diagnostic Approaches to Therapeutic Intervention. Int J Mol Sci 2020; 21:E6856. [PMID: 32962091 PMCID: PMC7555921 DOI: 10.3390/ijms21186856] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/15/2020] [Accepted: 09/15/2020] [Indexed: 12/11/2022] Open
Abstract
Fibroblast growth factor receptors (FGFRs) are tyrosine kinase receptors involved in many biological processes. Deregulated FGFR signaling plays an important role in tumor development and progression in different cancer types. FGFR genomic alterations, including FGFR gene fusions that originate by chromosomal rearrangements, represent a promising therapeutic target. Next-generation-sequencing (NGS) approaches have significantly improved the discovery of FGFR gene fusions and their detection in clinical samples. A variety of FGFR inhibitors have been developed, and several studies are trying to evaluate the efficacy of these agents in molecularly selected patients carrying FGFR genomic alterations. In this review, we describe the most frequent FGFR aberrations in human cancer. We also discuss the different approaches employed for the detection of FGFR fusions and the potential role of these genomic alterations as prognostic/predictive biomarkers.
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Affiliation(s)
- Antonella De Luca
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (A.D.L.); (R.E.A.); (A.M.R.); (M.R.M.); (C.E.)
| | - Riziero Esposito Abate
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (A.D.L.); (R.E.A.); (A.M.R.); (M.R.M.); (C.E.)
| | - Anna Maria Rachiglio
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (A.D.L.); (R.E.A.); (A.M.R.); (M.R.M.); (C.E.)
| | - Monica Rosaria Maiello
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (A.D.L.); (R.E.A.); (A.M.R.); (M.R.M.); (C.E.)
| | - Claudia Esposito
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (A.D.L.); (R.E.A.); (A.M.R.); (M.R.M.); (C.E.)
| | - Clorinda Schettino
- Clinical Trials Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy;
| | - Francesco Izzo
- Division of Surgical Oncology, Hepatobiliary Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy;
| | - Guglielmo Nasti
- SSD Innovative Therapies for Abdominal Cancers, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy;
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori-IRCCS-Fondazione G. Pascale, 80131 Naples, Italy; (A.D.L.); (R.E.A.); (A.M.R.); (M.R.M.); (C.E.)
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18
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Nerurkar SN, Goh D, Cheung CCL, Nga PQY, Lim JCT, Yeong JPS. Transcriptional Spatial Profiling of Cancer Tissues in the Era of Immunotherapy: The Potential and Promise. Cancers (Basel) 2020; 12:E2572. [PMID: 32917035 PMCID: PMC7563386 DOI: 10.3390/cancers12092572] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/05/2020] [Accepted: 09/06/2020] [Indexed: 12/18/2022] Open
Abstract
Intratumoral heterogeneity poses a major challenge to making an accurate diagnosis and establishing personalized treatment strategies for cancer patients. Moreover, this heterogeneity might underlie treatment resistance, disease progression, and cancer relapse. For example, while immunotherapies can confer a high success rate, selective pressures coupled with dynamic evolution within a tumour can drive the emergence of drug-resistant clones that allow tumours to persist in certain patients. To improve immunotherapy efficacy, researchers have used transcriptional spatial profiling techniques to identify and subsequently block the source of tumour heterogeneity. In this review, we describe and assess the different technologies available for such profiling within a cancer tissue. We first outline two well-known approaches, in situ hybridization and digital spatial profiling. Then, we highlight the features of an emerging technology known as Visium Spatial Gene Expression Solution. Visium generates quantitative gene expression data and maps them to the tissue architecture. By retaining spatial information, we are well positioned to identify novel biomarkers and perform computational analyses that might inform on novel combinatorial immunotherapies.
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Affiliation(s)
- Sanjna Nilesh Nerurkar
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore;
| | - Denise Goh
- Institute of Molecular and Cell Biology (IMCB), Agency of Science, Technology and Research (A*STAR), Singapore 169856, Singapore; (D.G.); (P.Q.Y.N.); (J.C.T.L.)
| | | | - Pei Qi Yvonne Nga
- Institute of Molecular and Cell Biology (IMCB), Agency of Science, Technology and Research (A*STAR), Singapore 169856, Singapore; (D.G.); (P.Q.Y.N.); (J.C.T.L.)
| | - Jeffrey Chun Tatt Lim
- Institute of Molecular and Cell Biology (IMCB), Agency of Science, Technology and Research (A*STAR), Singapore 169856, Singapore; (D.G.); (P.Q.Y.N.); (J.C.T.L.)
| | - Joe Poh Sheng Yeong
- Institute of Molecular and Cell Biology (IMCB), Agency of Science, Technology and Research (A*STAR), Singapore 169856, Singapore; (D.G.); (P.Q.Y.N.); (J.C.T.L.)
- Department of Anatomical Pathology, Singapore General Hospital, Singapore 169856, Singapore
- Singapore Immunology Network (SIgN), Agency of Science, Technology and Research (A*STAR), Singapore 138648, Singapore
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19
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Suster D, Suster S. The role of needle core biopsies in the evaluation of thymic epithelial neoplasms. J Am Soc Cytopathol 2020; 9:346-358. [PMID: 32467048 DOI: 10.1016/j.jasc.2020.04.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 04/15/2020] [Accepted: 04/16/2020] [Indexed: 12/14/2022]
Abstract
Thymic epithelial neoplasms are rare tumors derived from thymic epithelium that most often present as large anterior mediastinal masses. The vast majority of thymic epithelial neoplasms fall under the diagnostic category of thymoma, with a smaller percentage qualifying for a diagnosis of thymic carcinoma. The ability to render a definitive diagnosis on these tumors is generally hampered by their deep location and close proximity to vital structures, which makes biopsy sampling for histopathologic evaluation difficult. In recent years, the trend in medicine has been to opt for the least invasive procedure to obtain tissue samples that, by definition, implies also obtaining smaller and smaller biopsies, resulting in lesser amounts of tissue available for examination. In the mediastinum, the most common modalities for procuring biopsy samples from mass lesions include fine-needle aspiration, percutaneous core needle biopsy and video-assisted thoracoscopic biopsy. In this review, we will deal only with the role and limitations of percutaneous core biopsies in the interpretation of thymic epithelial neoplasms.
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Affiliation(s)
- David Suster
- Departments of Pathology, Mount Sinai Hospital and Icahn School of Medicine, New York City, New York
| | - Saul Suster
- Department of Pathology, Medical College of Wisconsin, Milwaukee, Wisconsin.
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20
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Computational analysis of pathological images enables a better diagnosis of TFE3 Xp11.2 translocation renal cell carcinoma. Nat Commun 2020; 11:1778. [PMID: 32286325 PMCID: PMC7156652 DOI: 10.1038/s41467-020-15671-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 03/23/2020] [Indexed: 12/17/2022] Open
Abstract
TFE3 Xp11.2 translocation renal cell carcinoma (TFE3-RCC) generally progresses more aggressively compared with other RCC subtypes, but it is challenging to diagnose TFE3-RCC by traditional visual inspection of pathological images. In this study, we collect hematoxylin and eosin- stained histopathology whole-slide images of 74 TFE3-RCC cases (the largest cohort to date) and 74 clear cell RCC cases (ccRCC, the most common RCC subtype) with matched gender and tumor grade. An automatic computational pipeline is implemented to extract image features. Comparative study identifies 52 image features with significant differences between TFE3-RCC and ccRCC. Machine learning models are built to distinguish TFE3-RCC from ccRCC. Tests of the classification models on an external validation set reveal high accuracy with areas under ROC curve ranging from 0.842 to 0.894. Our results suggest that automatically derived image features can capture subtle morphological differences between TFE3-RCC and ccRCC and contribute to a potential guideline for TFE3-RCC diagnosis. Translocation renal cell carcinoma is an aggressive form of renal cancer that is often misdiagnosed to other subtypes. Here the authors demonstrated that by using machine learning and H&E stained whole-slide images, an accurate diagnose of this particular type of renal cancer can be achieved.
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21
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Papillary Renal Neoplasm With Reverse Polarity: A Morphologic, Immunohistochemical, and Molecular Study. Am J Surg Pathol 2020; 43:1099-1111. [PMID: 31135486 DOI: 10.1097/pas.0000000000001288] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
We evaluated the clinicopathologic and chromosomal characteristics of a distinct subset of papillary renal tumors and compared them to a control series of papillary renal cell carcinoma types 1 and 2. Of the 18 patients, 9 were women and 9 were men, ranging in age from 46 to 80 years (mean, 64 y; median, 66 y). The tumors ranged in diameter from 0.6 to 3 cm (mean, 1.63 cm; median, 1.4 cm). Fourteen tumors were WHO/ISUP grade 2 and 4 were grade 1. All were stage category pT1. The tumors had branching papillae with thin fibrovascular cores, covered by cuboidal to columnar cells with granular eosinophilic cytoplasm, smooth luminal borders, and mostly regular and apically located nuclei with occasional nuclear clearing and inconspicuous nucleoli. Tubule formation and clear cytoplasmic vacuoles were observed in 5 and 9 tumors, respectively. Ten tumors had pseudocapsules. Psammoma bodies, necrosis, mitotic figures and intracellular hemosiderin are absent from all tumors. In contrast, papillary renal cell carcinoma type 1 consisted of delicate papillae covered by a single layer of cells with scanty pale cytoplasm with nuclei generally located in a single layer on the basement membrane of the papillary cores, while type 2 tumors had broad papillae covered by pseudostratified cells with eosinophilic cytoplasm and more randomly located nuclei. Both had occasional psammoma bodies, foamy macrophages and intracellular hemosiderin. Immunohistochemically, all were positive for pancytokeratin AE1/AE3, epithelial membrane antigen, MUC1, CD10, GATA3, and L1CAM. Cytokeratin 7 was positive in 16 tumors (1 had <5% positivity). CD117 and vimentin were always negative. α-methylacyl-CoA-racemase (AMACR/p504s) showed variable staining (range, 10% to 80%) in 5 tumors. However, all tumors in the control group were negative for GATA3 and positive for AMACR/p504s and vimentin immunostains. Fluorescence in situ hybridization analysis of the study group demonstrated chromosome 7 trisomy in 5 tumors (33%), trisomy 17 in 5 tumors (33%), and trisomy 7 and 17 in 3 tumors (20%). Chromosome Y deletion was found in 1 of 7 male patients and chromosome 3p was present in all tumors. No tumor recurrence or metastasis occurred. In summary, we propose the term papillary renal neoplasm with reverse polarity for this entity.
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22
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Al-Obaidy KI, Chovanec M, Cheng L. Molecular characteristics of testicular germ cell tumors: pathogenesis and mechanisms of therapy resistance. Expert Rev Anticancer Ther 2020; 20:75-79. [PMID: 31951790 DOI: 10.1080/14737140.2020.1717337] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Khaleel I Al-Obaidy
- Department of Pathology, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Pathology, College of Medicine, Imam Abdulrahman bin Faisal University, Dammam, Saudi Arabia
| | - Michal Chovanec
- 2nd Department of Oncology, Faculty of Medicine, Comenius University and National Cancer Institute, 83310, Bratislava, Slovakia
| | - Liang Cheng
- Department of Pathology, Indiana University School of Medicine, Indianapolis, IN, USA.,Department of Urology, Indiana University School of Medicine, Indianapolis, IN, USA
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23
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MYB-NFIB gene fusion in prostatic basal cell carcinoma: clinicopathologic correlates and comparison with basal cell adenoma and florid basal cell hyperplasia. Mod Pathol 2019; 32:1666-1674. [PMID: 31189999 DOI: 10.1038/s41379-019-0297-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/29/2019] [Accepted: 05/06/2019] [Indexed: 11/08/2022]
Abstract
Prostatic basal cell carcinoma is a malignant neoplasm composed of basaloid cells forming infiltrative nests and tubules, which may potentially be misdiagnosed as benign basal cell proliferations (i.e., florid basal cell hyperplasia or basal cell adenoma) and also closely resembles adenoid cystic carcinoma of the salivary gland. MYB-NFIB gene rearrangement occurs in 30-86% of salivary gland adenoid cystic carcinomas. We sought to further characterize MYB gene rearrangement in prostatic basal cell carcinoma and correlate MYB-NFIB fusion status with other clinicopathologic characteristics. To this end, FISH analysis for MYB-NFIB gene fusion using fusion probes was performed on formalin-fixed, paraffin-embedded tissue sections from prostatic basal cell carcinoma (n = 30), florid basal cell hyperplasia (n = 18), and basal cell adenoma (n = 4). Fourteen of 30 (47%) cases of basal cell carcinoma were positive for MYB-NFIB gene fusion FISH, and no cases of benign basal cell proliferations were positive (p < 0.05). FISH-positive patients (mean age = 63 years, range: 35-81) tended to be younger than FISH-negative patients (mean age = 70 years, range: 55-93). Most FISH-positive cases demonstrated adenoid cystic carcinoma-like morphology (57%), and most FISH-negative cases demonstrated nonadenoid cystic carcinoma-like morphology (93%); one case (FISH-positive) demonstrated areas with both adenoid cystic carcinoma-like and nonadenoid cystic carcinoma-like morphology. FISH-positive cases more frequently demonstrated perineural invasion (50% vs. 14%, p < 0.05) compared to FISH-negative cases. Conversely, tall basal cells (i.e., neoplastic cells at least two times taller than wide) were more frequent in FISH-negative cases than FISH-positive cases (93% vs. 36%, p < 0.05). Approximately, 50% of prostatic basal cell carcinoma harbor MYB-NFIB gene fusion. The majority of these cases were characterized by adenoid cystic carcinoma-like morphology, perineural invasion, and lack tall basal cells. Florid basal cell hyperplasia and basal cell adenoma are negative for MYB-NFIB gene fusion.
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24
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Mombaerts I, Ramberg I, Coupland SE, Heegaard S. Diagnosis of orbital mass lesions: clinical, radiological, and pathological recommendations. Surv Ophthalmol 2019; 64:741-756. [PMID: 31276737 DOI: 10.1016/j.survophthal.2019.06.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 06/21/2019] [Accepted: 06/24/2019] [Indexed: 02/07/2023]
Abstract
The orbit can harbor mass lesions of various cellular origins. The symptoms vary considerably according to the nature, location, and extent of the disease and include common signs of proptosis, globe displacement, eyelid swelling, and restricted eye motility. Although radiological imaging tools are improving, with each imaging pattern having its own differential diagnosis, orbital mass lesions often pose a diagnostic challenge. To provide an accurate, specific, and sufficiently comprehensive diagnosis, to optimize clinical management and estimate prognosis, pathological examination of a tissue biopsy is essential. Diagnostic orbital tissue biopsy is obtained through a minimally invasive orbitotomy procedure or, in selected cases, fine needle aspiration. The outcome of successful biopsy, however, is centered on its representativeness, processing, and interpretation. Owing to the often small volume of the orbital biopsies, artifacts in the specimens should be limited by careful peroperative tissue handling, fixation, processing, and storage. Some orbital lesions can be characterized on the basis of cytomorphology alone, whereas others need ancillary molecular testing to render the most reliable diagnosis of therapeutic, prognostic, and predictive value. Herein, we review the diagnostic algorithm for orbital mass lesions, using clinical, radiological, and pathological recommendations, and discuss the methods and potential pitfalls in orbital tissue biopsy acquisition and analysis.
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Affiliation(s)
- Ilse Mombaerts
- Department of Ophthalmology, University Hospitals Leuven, Leuven, Belgium.
| | - Ingvild Ramberg
- Department of Ophthalmology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark; Section of Eye Pathology, Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Sarah E Coupland
- Department of Cellular and Molecular Pathology, University of Liverpool, Liverpool, UK; Liverpool Clinical Laboratories, Royal Liverpool University Hospital, Liverpool, UK
| | - Steffen Heegaard
- Department of Ophthalmology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark; Section of Eye Pathology, Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
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Hsiao SJ, Zehir A, Sireci AN, Aisner DL. Detection of Tumor NTRK Gene Fusions to Identify Patients Who May Benefit from Tyrosine Kinase (TRK) Inhibitor Therapy. J Mol Diagn 2019; 21:553-571. [PMID: 31075511 PMCID: PMC7456740 DOI: 10.1016/j.jmoldx.2019.03.008] [Citation(s) in RCA: 143] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/17/2019] [Accepted: 03/01/2019] [Indexed: 01/04/2023] Open
Abstract
Chromosomal rearrangements involving the NTRK1, NTRK2, and NTRK3 genes (NTRK genes), which encode the high-affinity nerve growth factor receptor (TRKA), brain-derived neurotrophic factor/neurotrophin-3 (BDNF/NT-3) growth factor receptor (TRKB), and neurotrophin-3 (NT-3) growth factor receptor (TRKC) tyrosine kinases (TRK proteins), act as oncogenic drivers in a broad range of pediatric and adult tumor types. NTRK gene fusions have been shown to be actionable genomic events that are predictive of response to TRK kinase inhibitors, making their routine detection an evolving clinical priority. In certain exceedingly rare tumor types, NTRK gene fusions may be seen in the overwhelming majority of cases, whereas in a range of common cancers, reported incidences are in the range of 0.1% to 2%. Herein, we review the structure of the three NTRK genes and the nature and incidence of NTRK gene fusions in different solid tumor types, and we summarize the clinical data showing the importance of identifying tumors harboring such genomic events. We also outline the laboratory techniques that can be used to diagnose NTRK gene fusions in clinical samples. Finally, we propose a diagnostic algorithm for solid tumors to facilitate the identification of patients with TRK fusion cancer. This algorithm accounts for the widely varying frequencies by tumor histology and the underlying prevalence of TRK expression in the absence of NTRK gene fusions and is based on a combination of fluorescence in situ hybridization, next-generation sequencing, and immunohistochemistry assays.
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Affiliation(s)
- Susan J Hsiao
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, New York
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Anthony N Sireci
- Department of Medical Affairs, Loxo Oncology, Inc., Stamford, Connecticut
| | - Dara L Aisner
- Department of Pathology, University of Colorado, Aurora, Colorado.
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Williamson SR, Grignon DJ, Calió A, Stohr BA, Eble JN, Cheng L. Reply to Chou et al 'Do significant TFE3 gene rearrangements occur in succinate dehydrogenase deficient renal cell carcinoma? Borderline FISH results should be interpreted with caution' Mod Pathol 2017; in press. Mod Pathol 2017; 30:1509-1511. [PMID: 28972584 DOI: 10.1038/modpathol.2017.84] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Sean R Williamson
- Department of Pathology and Laboratory Medicine, Henry Ford Health System, Detroit, Michigan, USA
| | - David J Grignon
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Anna Calió
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA.,Department of Pathology, University of Verona, Verona, Italy
| | - Bradley A Stohr
- Department of Pathology, University of California San Francisco, San Francisco, California, USA
| | - John N Eble
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - Liang Cheng
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, USA
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Sanfrancesco JM, Eble JN, Grignon DJ, Wang M, Zhang S, Sundaram CP, Idrees MT, Pili R, Kouba E, Cheng L. Preservation of truncal genomic alterations in clear cell and papillary renal cell carcinomas with sarcomatoid features: An intra- and intertumoral, multifocal fluorescence in situ hybridization analysis reveals limited genetic heterogeneity. Mol Carcinog 2017; 56:2527-2537. [DOI: 10.1002/mc.22699] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 06/19/2017] [Accepted: 06/29/2017] [Indexed: 01/12/2023]
Affiliation(s)
- Joseph M. Sanfrancesco
- Departments of Pathology and Laboratory Medicine; Indiana University School of Medicine; Indianapolis Indiana
| | - John N. Eble
- Departments of Pathology and Laboratory Medicine; Indiana University School of Medicine; Indianapolis Indiana
| | - David J. Grignon
- Departments of Pathology and Laboratory Medicine; Indiana University School of Medicine; Indianapolis Indiana
| | - Mingsheng Wang
- Departments of Pathology and Laboratory Medicine; Indiana University School of Medicine; Indianapolis Indiana
| | - Shaobo Zhang
- Departments of Pathology and Laboratory Medicine; Indiana University School of Medicine; Indianapolis Indiana
| | - Chandru P. Sundaram
- Departments of Urology; Indiana University School of Medicine; Indianapolis Indiana
| | - Muhammad T. Idrees
- Departments of Pathology and Laboratory Medicine; Indiana University School of Medicine; Indianapolis Indiana
| | - Roberto Pili
- Departments of Medicine; Indiana University School of Medicine; Indianapolis Indiana
| | - Erik Kouba
- Departments of Pathology and Laboratory Medicine; Indiana University School of Medicine; Indianapolis Indiana
| | - Liang Cheng
- Departments of Pathology and Laboratory Medicine; Indiana University School of Medicine; Indianapolis Indiana
- Departments of Urology; Indiana University School of Medicine; Indianapolis Indiana
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